HEADER HYDROLASE 13-MAY-09 3HG4
TITLE HUMAN ALPHA-GALACTOSIDASE CATALYTIC MECHANISM 3. COVALENT INTERMEDIATE
CAVEAT 3HG4 7JZ B 802 HAS WRONG CHIRALITY AT ATOM C1 GAL B 803 HAS WRONG
CAVEAT 2 3HG4 CHIRALITY AT ATOM C4
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE A;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: ALPHA-D-GALACTOSIDE GALACTOHYDROLASE, ALPHA-D-GALACTOSIDASE
COMPND 5 A, MELIBIASE;
COMPND 6 EC: 3.2.1.22;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: GLA;
SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606
KEYWDS GLYCOPROTEIN, CARBOHYDRATE-BINDING PROTEIN, GLYCOSIDASE, LYSOSOMAL
KEYWDS 2 ENZYME, (BETA/ALPHA)8 BARREL, DISEASE MUTATION, DISULFIDE BOND,
KEYWDS 3 HYDROLASE, LYSOSOME
EXPDTA X-RAY DIFFRACTION
AUTHOR A.I.GUCE,N.E.CLARK,S.C.GARMAN
REVDAT 6 03-APR-24 3HG4 1 HETSYN
REVDAT 5 29-JUL-20 3HG4 1 CAVEAT COMPND REMARK HETNAM
REVDAT 5 2 1 LINK SITE ATOM
REVDAT 4 01-NOV-17 3HG4 1 REMARK
REVDAT 3 13-JUL-11 3HG4 1 VERSN
REVDAT 2 23-FEB-10 3HG4 1 JRNL
REVDAT 1 24-NOV-09 3HG4 0
JRNL AUTH A.I.GUCE,N.E.CLARK,E.N.SALGADO,D.R.IVANEN,A.A.KULMINSKAYA,
JRNL AUTH 2 H.BRUMER,S.C.GARMAN
JRNL TITL CATALYTIC MECHANISM OF HUMAN ALPHA-GALACTOSIDASE.
JRNL REF J.BIOL.CHEM. V. 285 3625 2010
JRNL REFN ISSN 0021-9258
JRNL PMID 19940122
JRNL DOI 10.1074/JBC.M109.060145
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.05
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 46268
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.166
REMARK 3 R VALUE (WORKING SET) : 0.165
REMARK 3 FREE R VALUE : 0.221
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100
REMARK 3 FREE R VALUE TEST SET COUNT : 949
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3198
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.44
REMARK 3 BIN R VALUE (WORKING SET) : 0.2150
REMARK 3 BIN FREE R VALUE SET COUNT : 73
REMARK 3 BIN FREE R VALUE : 0.2810
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6261
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 307
REMARK 3 SOLVENT ATOMS : 682
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 51.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.85
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.00000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.254
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.522
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6767 ; 0.008 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9221 ; 1.159 ; 1.988
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 780 ; 5.882 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 319 ;37.363 ;24.295
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1053 ;14.292 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;13.572 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1000 ; 0.077 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5080 ; 0.003 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3316 ; 0.186 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4552 ; 0.306 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 654 ; 0.121 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 50 ; 0.168 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.133 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4029 ; 0.375 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6234 ; 0.609 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3222 ; 1.058 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2987 ; 1.828 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1
REMARK 3
REMARK 3 NCS GROUP NUMBER : 1
REMARK 3 CHAIN NAMES : A B
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 A 32 A 328 4
REMARK 3 1 B 32 B 328 4
REMARK 3 2 A 329 A 421 4
REMARK 3 2 B 329 B 421 4
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
REMARK 3 MEDIUM POSITIONAL 1 A (A): 3122 ; 0.360 ; 0.500
REMARK 3 MEDIUM THERMAL 1 A (A**2): 3122 ; 0.320 ; 2.000
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3HG4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-09.
REMARK 100 THE DEPOSITION ID IS D_1000053091.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : OSMIC BLUE
REMARK 200 OPTICS : OSMIC BLUE
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46337
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 15.90
REMARK 200 R MERGE (I) : 0.11200
REMARK 200 R SYM (I) : 0.11200
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.3280
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 16.00
REMARK 200 R MERGE FOR SHELL (I) : 0.94400
REMARK 200 R SYM FOR SHELL (I) : 0.94400
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: HUMAN ALPHA-GALACTOSIDASE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.12
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, AMMONIUM SULFATE, SODIUM
REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 144.41000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.20500
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.20500
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 144.41000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 7190 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 31280 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 19.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLN A 422
REMARK 465 MET A 423
REMARK 465 SER A 424
REMARK 465 LEU A 425
REMARK 465 LYS A 426
REMARK 465 ASP A 427
REMARK 465 LEU A 428
REMARK 465 LEU A 429
REMARK 465 SER B 424
REMARK 465 LEU B 425
REMARK 465 LYS B 426
REMARK 465 ASP B 427
REMARK 465 LEU B 428
REMARK 465 LEU B 429
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 MET A 51 -137.15 58.78
REMARK 500 ASP A 92 -151.05 -105.44
REMARK 500 CYS A 94 32.33 72.46
REMARK 500 ASP A 266 -177.86 89.91
REMARK 500 ASN A 272 -131.84 -99.38
REMARK 500 MET B 51 -133.02 51.66
REMARK 500 ASP B 92 -151.23 -99.70
REMARK 500 CYS B 94 36.60 79.98
REMARK 500 CYS B 174 79.13 -151.02
REMARK 500 PHE B 211 -62.87 -108.92
REMARK 500 ASP B 266 177.98 90.62
REMARK 500 ASN B 272 -130.62 -98.49
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3HG2 RELATED DB: PDB
REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 1. EMPTY ACTIVE SITE
REMARK 900 RELATED ID: 3HF3 RELATED DB: PDB
REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 2. SUBSTRATE BOUND
REMARK 900 RELATED ID: 3HG5 RELATED DB: PDB
REMARK 900 HUMAN ALPHA-GALACTOSIDASE MECHANISM 4. PRODUCT BOUND
REMARK 900 RELATED ID: 1R46 RELATED DB: PDB
REMARK 900 RELATED ID: 1R47 RELATED DB: PDB
DBREF 3HG4 A 32 429 UNP P06280 AGAL_HUMAN 32 429
DBREF 3HG4 B 32 429 UNP P06280 AGAL_HUMAN 32 429
SEQRES 1 A 398 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP
SEQRES 2 A 398 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN
SEQRES 3 A 398 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET
SEQRES 4 A 398 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP
SEQRES 5 A 398 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET
SEQRES 6 A 398 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP
SEQRES 7 A 398 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN
SEQRES 8 A 398 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA
SEQRES 9 A 398 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER
SEQRES 10 A 398 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP
SEQRES 11 A 398 TRP GLY VAL ASP LEU LEU LYS PHE ASP GLY CYS TYR CYS
SEQRES 12 A 398 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET
SEQRES 13 A 398 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR
SEQRES 14 A 398 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS
SEQRES 15 A 398 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP
SEQRES 16 A 398 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE
SEQRES 17 A 398 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG
SEQRES 18 A 398 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO
SEQRES 19 A 398 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN
SEQRES 20 A 398 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA
SEQRES 21 A 398 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER
SEQRES 22 A 398 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE
SEQRES 23 A 398 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN
SEQRES 24 A 398 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO
SEQRES 25 A 398 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG
SEQRES 26 A 398 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL
SEQRES 27 A 398 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS
SEQRES 28 A 398 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY
SEQRES 29 A 398 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN
SEQRES 30 A 398 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET
SEQRES 31 A 398 GLN MET SER LEU LYS ASP LEU LEU
SEQRES 1 B 398 LEU ASP ASN GLY LEU ALA ARG THR PRO THR MET GLY TRP
SEQRES 2 B 398 LEU HIS TRP GLU ARG PHE MET CYS ASN LEU ASP CYS GLN
SEQRES 3 B 398 GLU GLU PRO ASP SER CYS ILE SER GLU LYS LEU PHE MET
SEQRES 4 B 398 GLU MET ALA GLU LEU MET VAL SER GLU GLY TRP LYS ASP
SEQRES 5 B 398 ALA GLY TYR GLU TYR LEU CYS ILE ASP ASP CYS TRP MET
SEQRES 6 B 398 ALA PRO GLN ARG ASP SER GLU GLY ARG LEU GLN ALA ASP
SEQRES 7 B 398 PRO GLN ARG PHE PRO HIS GLY ILE ARG GLN LEU ALA ASN
SEQRES 8 B 398 TYR VAL HIS SER LYS GLY LEU LYS LEU GLY ILE TYR ALA
SEQRES 9 B 398 ASP VAL GLY ASN LYS THR CYS ALA GLY PHE PRO GLY SER
SEQRES 10 B 398 PHE GLY TYR TYR ASP ILE ASP ALA GLN THR PHE ALA ASP
SEQRES 11 B 398 TRP GLY VAL ASP LEU LEU LYS PHE ASP GLY CYS TYR CYS
SEQRES 12 B 398 ASP SER LEU GLU ASN LEU ALA ASP GLY TYR LYS HIS MET
SEQRES 13 B 398 SER LEU ALA LEU ASN ARG THR GLY ARG SER ILE VAL TYR
SEQRES 14 B 398 SER CYS GLU TRP PRO LEU TYR MET TRP PRO PHE GLN LYS
SEQRES 15 B 398 PRO ASN TYR THR GLU ILE ARG GLN TYR CYS ASN HIS TRP
SEQRES 16 B 398 ARG ASN PHE ALA ASP ILE ASP ASP SER TRP LYS SER ILE
SEQRES 17 B 398 LYS SER ILE LEU ASP TRP THR SER PHE ASN GLN GLU ARG
SEQRES 18 B 398 ILE VAL ASP VAL ALA GLY PRO GLY GLY TRP ASN ASP PRO
SEQRES 19 B 398 ASP MET LEU VAL ILE GLY ASN PHE GLY LEU SER TRP ASN
SEQRES 20 B 398 GLN GLN VAL THR GLN MET ALA LEU TRP ALA ILE MET ALA
SEQRES 21 B 398 ALA PRO LEU PHE MET SER ASN ASP LEU ARG HIS ILE SER
SEQRES 22 B 398 PRO GLN ALA LYS ALA LEU LEU GLN ASP LYS ASP VAL ILE
SEQRES 23 B 398 ALA ILE ASN GLN ASP PRO LEU GLY LYS GLN GLY TYR GLN
SEQRES 24 B 398 LEU ARG GLN GLY ASP ASN PHE GLU VAL TRP GLU ARG PRO
SEQRES 25 B 398 LEU SER GLY LEU ALA TRP ALA VAL ALA MET ILE ASN ARG
SEQRES 26 B 398 GLN GLU ILE GLY GLY PRO ARG SER TYR THR ILE ALA VAL
SEQRES 27 B 398 ALA SER LEU GLY LYS GLY VAL ALA CYS ASN PRO ALA CYS
SEQRES 28 B 398 PHE ILE THR GLN LEU LEU PRO VAL LYS ARG LYS LEU GLY
SEQRES 29 B 398 PHE TYR GLU TRP THR SER ARG LEU ARG SER HIS ILE ASN
SEQRES 30 B 398 PRO THR GLY THR VAL LEU LEU GLN LEU GLU ASN THR MET
SEQRES 31 B 398 GLN MET SER LEU LYS ASP LEU LEU
MODRES 3HG4 ASN A 139 ASN GLYCOSYLATION SITE
MODRES 3HG4 ASN A 192 ASN GLYCOSYLATION SITE
MODRES 3HG4 ASN A 215 ASN GLYCOSYLATION SITE
MODRES 3HG4 ASN B 139 ASN GLYCOSYLATION SITE
MODRES 3HG4 ASN B 192 ASN GLYCOSYLATION SITE
MODRES 3HG4 ASN B 215 ASN GLYCOSYLATION SITE
HET NAG C 1 14
HET NAG C 2 14
HET FUC C 3 10
HET NAG D 1 14
HET NAG D 2 14
HET BMA D 3 11
HET MAN D 4 11
HET MAN D 5 11
HET NAG E 1 14
HET NAG E 2 14
HET NAG F 1 14
HET NAG F 2 14
HET FUC F 3 10
HET NAG G 1 14
HET NAG G 2 14
HET BMA G 3 11
HET MAN G 4 11
HET MAN G 5 11
HET 7JZ A 801 12
HET SO4 A 823 5
HET ACY A 842 4
HET ACY A 843 4
HET NAG B 715 14
HET 7JZ B 802 12
HET GAL B 803 12
HET SO4 B 821 5
HET SO4 B 822 5
HET ACY B 841 4
HET ACY B 844 4
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM FUC ALPHA-L-FUCOPYRANOSE
HETNAM BMA BETA-D-MANNOPYRANOSE
HETNAM MAN ALPHA-D-MANNOPYRANOSE
HETNAM 7JZ 2-DEOXY-2,2-DIFLUORO-BETA-D-LYXO-HEXOPYRANOSE
HETNAM SO4 SULFATE ION
HETNAM ACY ACETIC ACID
HETNAM GAL BETA-D-GALACTOPYRANOSE
HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA-
HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO-
HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE
HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L-
HETSYN 2 FUC FUCOSE; FUCOSE
HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE
HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE
HETSYN 7JZ 2-DEOXY-2,2-DIFLUORO-BETA-D-GALACTOPYRANOSYL-ENZYME
HETSYN 2 7JZ INTERMEDIATE; 2-DEOXY-2,2-DIFLUORO-BETA-D-LYXO-HEXOSE;
HETSYN 3 7JZ 2-DEOXY-2,2-DIFLUORO-D-LYXO-HEXOSE; 2-DEOXY-2,2-
HETSYN 4 7JZ DIFLUORO-LYXO-HEXOSE
HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE
FORMUL 3 NAG 11(C8 H15 N O6)
FORMUL 3 FUC 2(C6 H12 O5)
FORMUL 4 BMA 2(C6 H12 O6)
FORMUL 4 MAN 4(C6 H12 O6)
FORMUL 8 7JZ 2(C6 H10 F2 O5)
FORMUL 9 SO4 3(O4 S 2-)
FORMUL 10 ACY 4(C2 H4 O2)
FORMUL 14 GAL C6 H12 O6
FORMUL 19 HOH *682(H2 O)
HELIX 1 1 HIS A 46 MET A 51 1 6
HELIX 2 2 SER A 65 GLU A 79 1 15
HELIX 3 3 HIS A 115 LYS A 127 1 13
HELIX 4 4 TYR A 151 TRP A 162 1 12
HELIX 5 5 SER A 176 THR A 194 1 19
HELIX 6 6 GLU A 203 TRP A 209 1 7
HELIX 7 7 ASN A 215 CYS A 223 1 9
HELIX 8 8 SER A 235 ASN A 249 1 15
HELIX 9 9 ASN A 249 VAL A 254 1 6
HELIX 10 10 SER A 276 MET A 290 1 15
HELIX 11 11 SER A 304 GLN A 312 1 9
HELIX 12 12 ASP A 313 GLN A 321 1 9
HELIX 13 13 ALA A 370 VAL A 376 5 7
HELIX 14 14 HIS B 46 MET B 51 1 6
HELIX 15 15 SER B 65 GLU B 79 1 15
HELIX 16 16 GLY B 80 GLY B 85 1 6
HELIX 17 17 HIS B 115 SER B 126 1 12
HELIX 18 18 TYR B 151 TRP B 162 1 12
HELIX 19 19 SER B 176 ARG B 193 1 18
HELIX 20 20 GLU B 203 TRP B 209 1 7
HELIX 21 21 ASN B 215 CYS B 223 1 9
HELIX 22 22 SER B 235 ASN B 249 1 15
HELIX 23 23 ASN B 249 VAL B 254 1 6
HELIX 24 24 SER B 276 MET B 290 1 15
HELIX 25 25 SER B 304 GLN B 312 1 9
HELIX 26 26 ASP B 313 GLN B 321 1 9
HELIX 27 27 ALA B 370 VAL B 376 5 7
SHEET 1 A 8 TRP A 262 ASP A 264 0
SHEET 2 A 8 HIS A 225 ARG A 227 1 N TRP A 226 O ASP A 264
SHEET 3 A 8 VAL A 199 CYS A 202 1 N CYS A 202 O HIS A 225
SHEET 4 A 8 LEU A 166 ASP A 170 1 N LEU A 167 O VAL A 199
SHEET 5 A 8 LYS A 130 ASP A 136 1 N ILE A 133 O LYS A 168
SHEET 6 A 8 TYR A 88 CYS A 90 1 N LEU A 89 O LYS A 130
SHEET 7 A 8 MET A 42 LEU A 45 1 N TRP A 44 O CYS A 90
SHEET 8 A 8 LEU A 294 MET A 296 1 O MET A 296 N LEU A 45
SHEET 1 B 6 TYR A 329 GLY A 334 0
SHEET 2 B 6 PHE A 337 PRO A 343 -1 O VAL A 339 N LEU A 331
SHEET 3 B 6 ALA A 348 ASN A 355 -1 O ALA A 352 N TRP A 340
SHEET 4 B 6 THR A 412 ASN A 419 -1 O LEU A 417 N TRP A 349
SHEET 5 B 6 ALA A 381 LEU A 388 -1 N LEU A 387 O LEU A 414
SHEET 6 B 6 ARG A 392 GLU A 398 -1 O ARG A 392 N GLN A 386
SHEET 1 C 2 ARG A 363 ALA A 368 0
SHEET 2 C 2 ARG A 402 ILE A 407 -1 O SER A 405 N TYR A 365
SHEET 1 D 8 TRP B 262 ASP B 264 0
SHEET 2 D 8 HIS B 225 ARG B 227 1 N TRP B 226 O ASP B 264
SHEET 3 D 8 VAL B 199 CYS B 202 1 N CYS B 202 O HIS B 225
SHEET 4 D 8 LEU B 166 ASP B 170 1 N LEU B 167 O VAL B 199
SHEET 5 D 8 LYS B 130 ASP B 136 1 N ALA B 135 O ASP B 170
SHEET 6 D 8 TYR B 88 CYS B 90 1 N LEU B 89 O GLY B 132
SHEET 7 D 8 MET B 42 LEU B 45 1 N TRP B 44 O CYS B 90
SHEET 8 D 8 LEU B 294 MET B 296 1 O MET B 296 N LEU B 45
SHEET 1 E 6 TYR B 329 GLY B 334 0
SHEET 2 E 6 PHE B 337 LEU B 344 -1 O VAL B 339 N LEU B 331
SHEET 3 E 6 ALA B 348 ASN B 355 -1 O ALA B 352 N TRP B 340
SHEET 4 E 6 THR B 412 THR B 420 -1 O LEU B 417 N TRP B 349
SHEET 5 E 6 ALA B 381 LEU B 388 -1 N LEU B 387 O LEU B 414
SHEET 6 E 6 ARG B 392 GLU B 398 -1 O ARG B 392 N GLN B 386
SHEET 1 F 2 ARG B 363 ALA B 368 0
SHEET 2 F 2 ARG B 402 ILE B 407 -1 O LEU B 403 N ILE B 367
SSBOND 1 CYS A 52 CYS A 94 1555 1555 2.02
SSBOND 2 CYS A 56 CYS A 63 1555 1555 2.04
SSBOND 3 CYS A 142 CYS A 172 1555 1555 2.02
SSBOND 4 CYS A 202 CYS A 223 1555 1555 2.02
SSBOND 5 CYS A 378 CYS A 382 1555 1555 2.03
SSBOND 6 CYS B 52 CYS B 94 1555 1555 2.04
SSBOND 7 CYS B 56 CYS B 63 1555 1555 2.02
SSBOND 8 CYS B 142 CYS B 172 1555 1555 2.02
SSBOND 9 CYS B 202 CYS B 223 1555 1555 2.03
SSBOND 10 CYS B 378 CYS B 382 1555 1555 2.04
LINK ND2 ASN A 139 C1 NAG C 1 1555 1555 1.45
LINK OD2 ASP A 170 C1 7JZ A 801 1555 1555 1.34
LINK ND2 ASN A 192 C1 NAG D 1 1555 1555 1.45
LINK ND2 ASN A 215 C1 NAG E 1 1555 1555 1.45
LINK ND2 ASN B 139 C1 NAG F 1 1555 1555 1.44
LINK OD2 ASP B 170 C1 7JZ B 802 1555 1555 1.33
LINK ND2 ASN B 192 C1 NAG G 1 1555 1555 1.44
LINK ND2 ASN B 215 C1 NAG B 715 1555 1555 1.45
LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45
LINK O6 NAG C 1 C1 FUC C 3 1555 1555 1.45
LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44
LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.44
LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.45
LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.44
LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45
LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.45
LINK O6 NAG F 1 C1 FUC F 3 1555 1555 1.45
LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.44
LINK O4 NAG G 2 C1 BMA G 3 1555 1555 1.44
LINK O3 BMA G 3 C1 MAN G 4 1555 1555 1.45
LINK O6 BMA G 3 C1 MAN G 5 1555 1555 1.46
CISPEP 1 ASN A 379 PRO A 380 0 1.46
CISPEP 2 LEU A 388 PRO A 389 0 5.21
CISPEP 3 ASN B 379 PRO B 380 0 1.99
CISPEP 4 LEU B 388 PRO B 389 0 2.82
CRYST1 90.218 90.218 216.615 90.00 90.00 120.00 P 32 2 1 12
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.011084 0.006400 0.000000 0.00000
SCALE2 0.000000 0.012799 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004616 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
