HEADER TRANSFERASE 07-AUG-13 4M4P
TITLE CRYSTAL STRUCTURE OF EPHA4 ECTODOMAIN
CAVEAT 4M4P NAG A 601 HAS WRONG CHIRALITY AT ATOM C1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: EPHRIN TYPE-A RECEPTOR 4;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 27-543;
COMPND 5 SYNONYM: EPH-LIKE KINASE 8, EK8, HEK8, TYROSINE-PROTEIN KINASE TYRO1,
COMPND 6 TYROSINE-PROTEIN KINASE RECEPTOR SEK;
COMPND 7 EC: 2.7.10.1;
COMPND 8 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: EPHA4, HEK8, SEK, TYRO1;
SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HIGH5;
SOURCE 10 EXPRESSION_SYSTEM_ORGAN: OVARY;
SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PACGP67
KEYWDS EPH RECEPTOR PROTEIN KINASE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.XU,D.TSVETKOVA-ROBEV,Y.XU,Y.GOLDGUR,Y.-P.CHAN,J.P.HIMANEN,
AUTHOR 2 D.B.NIKOLOV
REVDAT 3 20-SEP-23 4M4P 1 HETSYN
REVDAT 2 29-JUL-20 4M4P 1 CAVEAT COMPND REMARK SEQADV
REVDAT 2 2 1 HETNAM LINK SITE ATOM
REVDAT 1 30-OCT-13 4M4P 0
JRNL AUTH K.XU,D.TZVETKOVA-ROBEV,Y.XU,Y.GOLDGUR,Y.P.CHAN,J.P.HIMANEN,
JRNL AUTH 2 D.B.NIKOLOV
JRNL TITL INSIGHTS INTO EPH RECEPTOR TYROSINE KINASE ACTIVATION FROM
JRNL TITL 2 CRYSTAL STRUCTURES OF THE EPHA4 ECTODOMAIN AND ITS COMPLEX
JRNL TITL 3 WITH EPHRIN-A5.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 14634 2013
JRNL REFN ISSN 0027-8424
JRNL PMID 23959867
JRNL DOI 10.1073/PNAS.1311000110
REMARK 2
REMARK 2 RESOLUTION. 2.08 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 42061
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.190
REMARK 3 R VALUE (WORKING SET) : 0.189
REMARK 3 FREE R VALUE : 0.225
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700
REMARK 3 FREE R VALUE TEST SET COUNT : 1978
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 27.1795 - 5.0048 0.99 2839 139 0.1773 0.1910
REMARK 3 2 5.0048 - 3.9764 1.00 2836 151 0.1556 0.1756
REMARK 3 3 3.9764 - 3.4749 1.00 2891 143 0.1764 0.2397
REMARK 3 4 3.4749 - 3.1577 1.00 2873 133 0.1989 0.2462
REMARK 3 5 3.1577 - 2.9317 1.00 2855 138 0.1984 0.2087
REMARK 3 6 2.9317 - 2.7590 1.00 2895 140 0.2041 0.2420
REMARK 3 7 2.7590 - 2.6210 1.00 2816 142 0.2010 0.2668
REMARK 3 8 2.6210 - 2.5070 1.00 2898 136 0.2105 0.2980
REMARK 3 9 2.5070 - 2.4105 1.00 2893 142 0.2020 0.2473
REMARK 3 10 2.4105 - 2.3274 1.00 2835 152 0.2127 0.2456
REMARK 3 11 2.3274 - 2.2546 1.00 2872 148 0.2147 0.2899
REMARK 3 12 2.2546 - 2.1902 1.00 2870 138 0.2296 0.2756
REMARK 3 13 2.1902 - 2.1326 1.00 2884 142 0.2306 0.2414
REMARK 3 14 2.1326 - 2.0806 1.00 2826 134 0.2445 0.2771
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.600
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 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.009 4155
REMARK 3 ANGLE : 1.355 5641
REMARK 3 CHIRALITY : 0.111 635
REMARK 3 PLANARITY : 0.007 732
REMARK 3 DIHEDRAL : 16.888 1541
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 66 )
REMARK 3 ORIGIN FOR THE GROUP (A): -33.1333 39.1031 -4.0756
REMARK 3 T TENSOR
REMARK 3 T11: 0.3597 T22: 0.3358
REMARK 3 T33: 0.4758 T12: -0.0376
REMARK 3 T13: 0.0821 T23: 0.1179
REMARK 3 L TENSOR
REMARK 3 L11: 1.9448 L22: 2.4852
REMARK 3 L33: 1.1342 L12: -1.9503
REMARK 3 L13: -1.0997 L23: 1.5229
REMARK 3 S TENSOR
REMARK 3 S11: 0.2234 S12: -0.1467 S13: 1.0018
REMARK 3 S21: -0.6548 S22: 0.0231 S23: -1.1005
REMARK 3 S31: -0.7816 S32: 0.3109 S33: 0.1223
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 202 )
REMARK 3 ORIGIN FOR THE GROUP (A): -38.1274 31.6006 3.3743
REMARK 3 T TENSOR
REMARK 3 T11: 0.2739 T22: 0.3127
REMARK 3 T33: 0.2693 T12: -0.0066
REMARK 3 T13: -0.0266 T23: 0.0580
REMARK 3 L TENSOR
REMARK 3 L11: 2.4881 L22: 3.4761
REMARK 3 L33: 1.5378 L12: -1.4618
REMARK 3 L13: -0.2327 L23: 0.2663
REMARK 3 S TENSOR
REMARK 3 S11: -0.0764 S12: -0.0017 S13: 0.1725
REMARK 3 S21: 0.1503 S22: 0.0175 S23: -0.2528
REMARK 3 S31: -0.0406 S32: 0.1550 S33: 0.0367
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 203 THROUGH 305 )
REMARK 3 ORIGIN FOR THE GROUP (A): 1.0773 10.2088 -4.2614
REMARK 3 T TENSOR
REMARK 3 T11: 0.2846 T22: 0.8937
REMARK 3 T33: 0.7452 T12: 0.0833
REMARK 3 T13: 0.0519 T23: -0.0007
REMARK 3 L TENSOR
REMARK 3 L11: 2.0811 L22: 0.7409
REMARK 3 L33: 1.1206 L12: -0.2725
REMARK 3 L13: 0.5171 L23: 0.2610
REMARK 3 S TENSOR
REMARK 3 S11: -0.0849 S12: 0.0697 S13: 0.2769
REMARK 3 S21: -0.1254 S22: 0.2177 S23: -0.5861
REMARK 3 S31: 0.0158 S32: 0.8388 S33: 0.1479
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 306 THROUGH 446 )
REMARK 3 ORIGIN FOR THE GROUP (A): 52.8931 -8.1458 -5.3091
REMARK 3 T TENSOR
REMARK 3 T11: 0.4965 T22: 1.1874
REMARK 3 T33: 1.3531 T12: 0.0159
REMARK 3 T13: -0.0949 T23: -0.6652
REMARK 3 L TENSOR
REMARK 3 L11: 0.9377 L22: 0.3039
REMARK 3 L33: 0.9336 L12: 0.0435
REMARK 3 L13: -0.4352 L23: -0.3980
REMARK 3 S TENSOR
REMARK 3 S11: 0.3153 S12: 1.3824 S13: -0.7429
REMARK 3 S21: -0.1733 S22: 0.0052 S23: 0.3780
REMARK 3 S31: 0.6575 S32: -0.8563 S33: 0.5315
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 447 THROUGH 542 )
REMARK 3 ORIGIN FOR THE GROUP (A): 70.9159 7.5305 15.8514
REMARK 3 T TENSOR
REMARK 3 T11: 0.3429 T22: 0.4020
REMARK 3 T33: 0.4305 T12: 0.0570
REMARK 3 T13: 0.0176 T23: -0.0005
REMARK 3 L TENSOR
REMARK 3 L11: 2.5054 L22: 2.5703
REMARK 3 L33: 3.3513 L12: 0.1733
REMARK 3 L13: 0.0334 L23: 1.7790
REMARK 3 S TENSOR
REMARK 3 S11: -0.0157 S12: 0.0169 S13: -0.6263
REMARK 3 S21: 0.1680 S22: 0.0528 S23: -0.2018
REMARK 3 S31: 0.3645 S32: 0.1523 S33: -0.0222
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE AUTHORS STATE THAT THE CONFORMATION
REMARK 3 ISSUE FOR NAG601A AS WELL AS THE HIGH REAL SPACE R-FACTORS FOR
REMARK 3 NAG601A AND NAG602A ARE DUE TO THE PARTIAL DISORDER. THE DENSITY
REMARK 3 IS OF POOR QUALITY AND THE MODEL PRIMARILY REFLECTS THAT THEY
REMARK 3 ARE THERE.
REMARK 4
REMARK 4 4M4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-13.
REMARK 100 THE DEPOSITION ID IS D_1000081462.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-FEB-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42061
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080
REMARK 200 RESOLUTION RANGE LOW (A) : 27.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
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) : 2.08
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.80
REMARK 200 R MERGE FOR SHELL (I) : 0.68000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 3FL7
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 61.05
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG400, 0.1M MES BUFFER PH 6.0, 3%
REMARK 280 DMSO, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32
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
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 33.03467
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 16.51733
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 ALA A 26
REMARK 465 ALA A 371
REMARK 465 GLY A 372
REMARK 465 ASP A 373
REMARK 465 GLY A 543
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 CB CYS A 369 SG CYS A 377 1.57
REMARK 500 N ASP A 61 O HOH A 758 1.95
REMARK 500 ND2 ASN A 340 C2 NAG A 602 1.99
REMARK 500 O HOH A 805 O HOH A 817 1.99
REMARK 500 OE2 GLU A 451 O HOH A 780 2.01
REMARK 500 O ILE A 444 O HOH A 800 2.08
REMARK 500 O HOH A 844 O HOH A 845 2.13
REMARK 500 O HOH A 749 O HOH A 757 2.17
REMARK 500 NH2 ARG A 489 O HOH A 717 2.18
REMARK 500 OG1 THR A 217 O HOH A 798 2.19
REMARK 500 O HOH A 793 O HOH A 816 2.19
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 GLU A 42 85.65 65.56
REMARK 500 ASN A 64 -63.40 -104.66
REMARK 500 ASN A 74 34.50 -95.95
REMARK 500 GLU A 92 -124.60 52.66
REMARK 500 ASN A 140 -57.71 -130.00
REMARK 500 LYS A 240 -65.56 -99.49
REMARK 500 SER A 270 -127.62 59.54
REMARK 500 GLU A 341 -116.41 51.21
REMARK 500 LYS A 376 -115.28 57.20
REMARK 500 CYS A 377 71.29 60.40
REMARK 500 TYR A 386 -3.73 85.06
REMARK 500 GLN A 389 -62.00 -126.98
REMARK 500 GLN A 390 -14.33 83.85
REMARK 500 SER A 420 -11.83 81.61
REMARK 500 ALA A 445 -14.65 68.50
REMARK 500 ASN A 533 -163.47 -116.33
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 LEU A 404 ALA A 405 -149.24
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4M4R RELATED DB: PDB
DBREF 4M4P A 27 543 UNP P54764 EPHA4_HUMAN 27 543
SEQADV 4M4P ALA A 26 UNP P54764 EXPRESSION TAG
SEQRES 1 A 518 ALA PRO ALA ASN GLU VAL THR LEU LEU ASP SER ARG SER
SEQRES 2 A 518 VAL GLN GLY GLU LEU GLY TRP ILE ALA SER PRO LEU GLU
SEQRES 3 A 518 GLY GLY TRP GLU GLU VAL SER ILE MET ASP GLU LYS ASN
SEQRES 4 A 518 THR PRO ILE ARG THR TYR GLN VAL CYS ASN VAL MET GLU
SEQRES 5 A 518 PRO SER GLN ASN ASN TRP LEU ARG THR ASP TRP ILE THR
SEQRES 6 A 518 ARG GLU GLY ALA GLN ARG VAL TYR ILE GLU ILE LYS PHE
SEQRES 7 A 518 THR LEU ARG ASP CYS ASN SER LEU PRO GLY VAL MET GLY
SEQRES 8 A 518 THR CYS LYS GLU THR PHE ASN LEU TYR TYR TYR GLU SER
SEQRES 9 A 518 ASP ASN ASP LYS GLU ARG PHE ILE ARG GLU ASN GLN PHE
SEQRES 10 A 518 VAL LYS ILE ASP THR ILE ALA ALA ASP GLU SER PHE THR
SEQRES 11 A 518 GLN VAL ASP ILE GLY ASP ARG ILE MET LYS LEU ASN THR
SEQRES 12 A 518 GLU ILE ARG ASP VAL GLY PRO LEU SER LYS LYS GLY PHE
SEQRES 13 A 518 TYR LEU ALA PHE GLN ASP VAL GLY ALA CYS ILE ALA LEU
SEQRES 14 A 518 VAL SER VAL ARG VAL PHE TYR LYS LYS CYS PRO LEU THR
SEQRES 15 A 518 VAL ARG ASN LEU ALA GLN PHE PRO ASP THR ILE THR GLY
SEQRES 16 A 518 ALA ASP THR SER SER LEU VAL GLU VAL ARG GLY SER CYS
SEQRES 17 A 518 VAL ASN ASN SER GLU GLU LYS ASP VAL PRO LYS MET TYR
SEQRES 18 A 518 CYS GLY ALA ASP GLY GLU TRP LEU VAL PRO ILE GLY ASN
SEQRES 19 A 518 CYS LEU CYS ASN ALA GLY HIS GLU GLU ARG SER GLY GLU
SEQRES 20 A 518 CYS GLN ALA CYS LYS ILE GLY TYR TYR LYS ALA LEU SER
SEQRES 21 A 518 THR ASP ALA THR CYS ALA LYS CYS PRO PRO HIS SER TYR
SEQRES 22 A 518 SER VAL TRP GLU GLY ALA THR SER CYS THR CYS ASP ARG
SEQRES 23 A 518 GLY PHE PHE ARG ALA ASP ASN ASP ALA ALA SER MET PRO
SEQRES 24 A 518 CYS THR ARG PRO PRO SER ALA PRO LEU ASN LEU ILE SER
SEQRES 25 A 518 ASN VAL ASN GLU THR SER VAL ASN LEU GLU TRP SER SER
SEQRES 26 A 518 PRO GLN ASN THR GLY GLY ARG GLN ASP ILE SER TYR ASN
SEQRES 27 A 518 VAL VAL CYS LYS LYS CYS GLY ALA GLY ASP PRO SER LYS
SEQRES 28 A 518 CYS ARG PRO CYS GLY SER GLY VAL HIS TYR THR PRO GLN
SEQRES 29 A 518 GLN ASN GLY LEU LYS THR THR LYS VAL SER ILE THR ASP
SEQRES 30 A 518 LEU LEU ALA HIS THR ASN TYR THR PHE GLU ILE TRP ALA
SEQRES 31 A 518 VAL ASN GLY VAL SER LYS TYR ASN PRO ASN PRO ASP GLN
SEQRES 32 A 518 SER VAL SER VAL THR VAL THR THR ASN GLN ALA ALA PRO
SEQRES 33 A 518 SER SER ILE ALA LEU VAL GLN ALA LYS GLU VAL THR ARG
SEQRES 34 A 518 TYR SER VAL ALA LEU ALA TRP LEU GLU PRO ASP ARG PRO
SEQRES 35 A 518 ASN GLY VAL ILE LEU GLU TYR GLU VAL LYS TYR TYR GLU
SEQRES 36 A 518 LYS ASP GLN ASN GLU ARG SER TYR ARG ILE VAL ARG THR
SEQRES 37 A 518 ALA ALA ARG ASN THR ASP ILE LYS GLY LEU ASN PRO LEU
SEQRES 38 A 518 THR SER TYR VAL PHE HIS VAL ARG ALA ARG THR ALA ALA
SEQRES 39 A 518 GLY TYR GLY ASP PHE SER GLU PRO LEU GLU VAL THR THR
SEQRES 40 A 518 ASN THR VAL PRO SER ARG ILE ILE GLY ASP GLY
MODRES 4M4P ASN A 340 ASN GLYCOSYLATION SITE
MODRES 4M4P ASN A 408 ASN GLYCOSYLATION SITE
MODRES 4M4P ASN A 235 ASN GLYCOSYLATION SITE
HET NAG B 1 14
HET NAG B 2 14
HET NAG A 601 14
HET NAG A 602 14
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
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
FORMUL 2 NAG 4(C8 H15 N O6)
FORMUL 5 HOH *161(H2 O)
HELIX 1 1 ASP A 107 LEU A 111 5 5
HELIX 2 2 ASP A 151 THR A 155 5 5
HELIX 3 3 ASN A 425 ASP A 427 5 3
SHEET 1 A 5 GLU A 30 ASP A 35 0
SHEET 2 A 5 ILE A 192 CYS A 204 -1 O VAL A 199 N LEU A 33
SHEET 3 A 5 VAL A 97 LEU A 105 -1 N TYR A 98 O PHE A 200
SHEET 4 A 5 ILE A 163 VAL A 173 -1 O ARG A 171 N ILE A 99
SHEET 5 A 5 GLN A 156 ASP A 158 -1 N ASP A 158 O ILE A 163
SHEET 1 B 4 GLU A 55 MET A 60 0
SHEET 2 B 4 PRO A 66 VAL A 72 -1 O GLN A 71 N GLU A 55
SHEET 3 B 4 ILE A 192 CYS A 204 -1 O LEU A 194 N TYR A 70
SHEET 4 B 4 THR A 217 ILE A 218 -1 O THR A 217 N CYS A 204
SHEET 1 C 4 ILE A 46 SER A 48 0
SHEET 2 C 4 ASN A 82 ARG A 85 -1 O TRP A 83 N SER A 48
SHEET 3 C 4 GLY A 180 ASP A 187 -1 O PHE A 185 N LEU A 84
SHEET 4 C 4 ILE A 89 THR A 90 -1 N ILE A 89 O PHE A 181
SHEET 1 D 5 ILE A 46 SER A 48 0
SHEET 2 D 5 ASN A 82 ARG A 85 -1 O TRP A 83 N SER A 48
SHEET 3 D 5 GLY A 180 ASP A 187 -1 O PHE A 185 N LEU A 84
SHEET 4 D 5 THR A 121 SER A 129 -1 N ASN A 123 O GLN A 186
SHEET 5 D 5 VAL A 143 ALA A 149 -1 O ILE A 145 N LEU A 124
SHEET 1 E 3 THR A 207 ARG A 209 0
SHEET 2 E 3 ALA A 212 PHE A 214 -1 O PHE A 214 N THR A 207
SHEET 3 E 3 SER A 232 CYS A 233 -1 O SER A 232 N GLN A 213
SHEET 1 F 3 LEU A 226 ARG A 230 0
SHEET 2 F 3 SER A 237 GLY A 248 -1 O CYS A 247 N VAL A 227
SHEET 3 F 3 ILE A 257 CYS A 262 -1 O LEU A 261 N GLU A 238
SHEET 1 G 2 HIS A 266 ARG A 269 0
SHEET 2 G 2 GLU A 272 ALA A 275 -1 O GLU A 272 N ARG A 269
SHEET 1 H 2 TYR A 280 TYR A 281 0
SHEET 2 H 2 ALA A 291 LYS A 292 -1 O ALA A 291 N TYR A 281
SHEET 1 I 2 SER A 297 TYR A 298 0
SHEET 2 I 2 THR A 308 CYS A 309 -1 O THR A 308 N TYR A 298
SHEET 1 J 4 LEU A 333 ASN A 340 0
SHEET 2 J 4 SER A 343 SER A 349 -1 O SER A 343 N ASN A 340
SHEET 3 J 4 LYS A 397 THR A 401 -1 O VAL A 398 N LEU A 346
SHEET 4 J 4 HIS A 385 THR A 387 -1 N THR A 387 O SER A 399
SHEET 1 K 3 SER A 361 LYS A 368 0
SHEET 2 K 3 ASN A 408 VAL A 416 -1 O VAL A 416 N SER A 361
SHEET 3 K 3 SER A 429 THR A 435 -1 O VAL A 430 N ILE A 413
SHEET 1 L 3 VAL A 447 VAL A 452 0
SHEET 2 L 3 VAL A 457 TRP A 461 -1 O ALA A 460 N GLN A 448
SHEET 3 L 3 ASN A 497 ILE A 500 -1 O THR A 498 N LEU A 459
SHEET 1 M 4 ARG A 489 THR A 493 0
SHEET 2 M 4 GLU A 473 GLU A 480 -1 N VAL A 476 O VAL A 491
SHEET 3 M 4 SER A 508 THR A 517 -1 O ARG A 514 N GLU A 475
SHEET 4 M 4 GLY A 520 TYR A 521 -1 O GLY A 520 N THR A 517
SHEET 1 N 4 ARG A 489 THR A 493 0
SHEET 2 N 4 GLU A 473 GLU A 480 -1 N VAL A 476 O VAL A 491
SHEET 3 N 4 SER A 508 THR A 517 -1 O ARG A 514 N GLU A 475
SHEET 4 N 4 LEU A 528 THR A 531 -1 O VAL A 530 N TYR A 509
SSBOND 1 CYS A 73 CYS A 191 1555 1555 2.08
SSBOND 2 CYS A 108 CYS A 118 1555 1555 2.06
SSBOND 3 CYS A 204 CYS A 247 1555 1555 2.09
SSBOND 4 CYS A 233 CYS A 260 1555 1555 2.07
SSBOND 5 CYS A 262 CYS A 273 1555 1555 2.05
SSBOND 6 CYS A 276 CYS A 290 1555 1555 2.03
SSBOND 7 CYS A 293 CYS A 307 1555 1555 2.05
SSBOND 8 CYS A 309 CYS A 325 1555 1555 2.03
SSBOND 9 CYS A 366 CYS A 380 1555 1555 2.02
SSBOND 10 CYS A 369 CYS A 377 1555 1555 2.04
LINK ND2 ASN A 235 C1 NAG A 601 1555 1555 1.45
LINK ND2 ASN A 340 C1 NAG A 602 1555 1555 1.44
LINK ND2 ASN A 408 C1 NAG B 1 1555 1555 1.45
LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44
CISPEP 1 LEU A 43 GLY A 44 0 -29.90
CISPEP 2 SER A 48 PRO A 49 0 -6.80
CISPEP 3 LYS A 63 ASN A 64 0 -9.96
CISPEP 4 GLY A 174 PRO A 175 0 -5.36
CISPEP 5 ASN A 235 ASN A 236 0 -7.46
CISPEP 6 GLY A 355 GLY A 356 0 -3.59
CISPEP 7 HIS A 385 TYR A 386 0 7.31
CISPEP 8 THR A 387 PRO A 388 0 -9.89
CRYST1 112.589 112.589 49.552 90.00 90.00 120.00 P 32 3
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 0.008882 0.005128 0.000000 0.00000
SCALE2 0.000000 0.010256 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020181 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
