HEADER T-CELL SURFACE GLYCOPROTEIN 26-JAN-94 1CDI
TITLE STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS
TITLE 2 REFINED IN TWO CRYSTAL LATTICES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: T CELL SURFACE GLYCOPROTEIN CD4;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606
KEYWDS T-CELL SURFACE GLYCOPROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.E.RYU,A.TRUNEH,R.W.SWEET,W.A.HENDRICKSON
REVDAT 5 14-AUG-19 1CDI 1 REMARK
REVDAT 4 17-JUL-19 1CDI 1 REMARK
REVDAT 3 24-FEB-09 1CDI 1 VERSN
REVDAT 2 01-APR-03 1CDI 1 JRNL
REVDAT 1 30-APR-94 1CDI 0
JRNL AUTH S.E.RYU,A.TRUNEH,R.W.SWEET,W.A.HENDRICKSON
JRNL TITL STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4
JRNL TITL 2 AS REFINED IN TWO CRYSTAL LATTICES.
JRNL REF STRUCTURE V. 2 59 1994
JRNL REFN ISSN 0969-2126
JRNL PMID 8075984
JRNL DOI 10.1016/S0969-2126(00)00008-3
REMARK 2
REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PROLSQ
REMARK 3 AUTHORS : KONNERT,HENDRICKSON
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 3235
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.183
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1390
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : NULL ; NULL
REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : NULL ; NULL
REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : NULL ; NULL
REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 0.440 ; 1.000
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.796 ; 1.500
REMARK 3 SIDE-CHAIN BOND (A**2) : 0.545 ; 1.500
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.910 ; 2.000
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1CDI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000172254.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.57
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
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 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 66.77500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.13500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 66.77500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.13500
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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 APPLY THE FOLLOWING TO CHAINS: A
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 350 BIOMT1 2 -1.000000 0.000000 0.000000 118.81527
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 137.42231
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 N GLN A 40 O PHE A 43 2.00
REMARK 500 O ASN A 164 N LYS A 166 2.07
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 LYS A 1 CA - CB - CG ANGL. DEV. = 13.4 DEGREES
REMARK 500 GLN A 20 N - CA - CB ANGL. DEV. = 15.2 DEGREES
REMARK 500 GLN A 20 CA - CB - CG ANGL. DEV. = 23.4 DEGREES
REMARK 500 THR A 45 N - CA - CB ANGL. DEV. = 14.7 DEGREES
REMARK 500 ASP A 56 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES
REMARK 500 ARG A 58 CD - NE - CZ ANGL. DEV. = 16.4 DEGREES
REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 THR A 81 N - CA - CB ANGL. DEV. = 16.1 DEGREES
REMARK 500 LEU A 95 N - CA - CB ANGL. DEV. = -12.9 DEGREES
REMARK 500 ARG A 134 CD - NE - CZ ANGL. DEV. = 16.7 DEGREES
REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
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 LYS A 1 92.62 -46.37
REMARK 500 ALA A 18 -82.75 -86.12
REMARK 500 SER A 19 21.99 85.71
REMARK 500 LYS A 21 128.06 -30.21
REMARK 500 SER A 31 -35.74 -37.10
REMARK 500 ASN A 32 22.59 -64.04
REMARK 500 GLN A 33 -17.75 53.18
REMARK 500 SER A 49 154.16 176.12
REMARK 500 SER A 60 -44.14 -28.97
REMARK 500 ASN A 73 71.70 38.08
REMARK 500 ASP A 78 8.14 -57.34
REMARK 500 GLU A 87 -77.00 35.73
REMARK 500 ASN A 103 8.42 -53.04
REMARK 500 SER A 104 -87.00 -111.77
REMARK 500 ASP A 105 -157.49 173.02
REMARK 500 SER A 125 60.51 -116.85
REMARK 500 ILE A 138 101.08 -169.21
REMARK 500 LEU A 151 -58.52 30.02
REMARK 500 ASP A 153 37.92 -88.70
REMARK 500 GLN A 163 -108.43 -117.48
REMARK 500 GLN A 165 -73.11 54.14
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1CDI A 0 178 UNP P01730 CD4_HUMAN 23 203
SEQADV 1CDI THR A 0 UNP P01730 GLY 25 CONFLICT
SEQRES 1 A 179 THR LYS LYS VAL VAL LEU GLY LYS LYS GLY ASP THR VAL
SEQRES 2 A 179 GLU LEU THR CYS THR ALA SER GLN LYS LYS SER ILE GLN
SEQRES 3 A 179 PHE HIS TRP LYS ASN SER ASN GLN ILE LYS ILE LEU GLY
SEQRES 4 A 179 ASN GLN GLY SER PHE LEU THR LYS GLY PRO SER LYS LEU
SEQRES 5 A 179 ASN ASP ARG ALA ASP SER ARG ARG SER LEU TRP ASP GLN
SEQRES 6 A 179 GLY ASN PHE PRO LEU ILE ILE LYS ASN LEU LYS ILE GLU
SEQRES 7 A 179 ASP SER ASP THR TYR ILE CYS GLU VAL GLU ASP GLN LYS
SEQRES 8 A 179 GLU GLU VAL GLN LEU LEU VAL PHE GLY LEU THR ALA ASN
SEQRES 9 A 179 SER ASP THR HIS LEU LEU GLN GLY GLN SER LEU THR LEU
SEQRES 10 A 179 THR LEU GLU SER PRO PRO GLY SER SER PRO SER VAL GLN
SEQRES 11 A 179 CYS ARG SER PRO ARG GLY LYS ASN ILE GLN GLY GLY LYS
SEQRES 12 A 179 THR LEU SER VAL SER GLN LEU GLU LEU GLN ASP SER GLY
SEQRES 13 A 179 THR TRP THR CYS THR VAL LEU GLN ASN GLN LYS LYS VAL
SEQRES 14 A 179 GLU PHE LYS ILE ASP ILE VAL VAL LEU ALA
HELIX 1 1 ARG A 58 GLY A 65 5 8
HELIX 2 2 LYS A 75 SER A 79 5 5
HELIX 3 3 GLU A 150 SER A 154 5 5
SHEET 1 D1A 3 ARG A 54 ARG A 58 0
SHEET 2 D1A 3 GLN A 64 LYS A 72 -1
SHEET 3 D1A 3 VAL A 12 ALA A 18 -1
SHEET 1 D1B 6 LYS A 2 LYS A 8 0
SHEET 2 D1B 6 GLN A 89 PHE A 98 1
SHEET 3 D1B 6 ASP A 80 VAL A 86 -1
SHEET 4 D1B 6 GLN A 25 SER A 31 -1
SHEET 5 D1B 6 ILE A 34 GLN A 40 -1
SHEET 6 D1B 6 PHE A 43 GLY A 47 -1
SHEET 1 D2A 3 LYS A 142 LEU A 149 0
SHEET 2 D2A 3 GLY A 111 GLU A 119 -1
SHEET 3 D2A 3 GLY A 99 ASN A 103 -1
SHEET 1 D2B 4 LYS A 166 ILE A 174 0
SHEET 2 D2B 4 GLY A 155 GLN A 163 -1
SHEET 3 D2B 4 SER A 127 SER A 132 -1
SHEET 4 D2B 4 LYS A 136 GLY A 140 -1
SSBOND 1 CYS A 16 CYS A 84 1555 1555 2.03
SSBOND 2 CYS A 130 CYS A 159 1555 1555 2.06
CRYST1 133.550 32.270 46.070 90.00 96.12 90.00 C 1 2 1 4
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 0.007488 0.000000 0.000803 0.00000
SCALE2 0.000000 0.030989 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021831 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
