HEADER PROTEIN BINDING 13-APR-22 7ZKR TITLE HUMAN GABARAP IN COMPLEX WITH STAPLED PEPTIDE PEN3-ORTHO COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GABA(A) RECEPTOR-ASSOCIATED PROTEIN,MM46; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PEN3-ORTHO; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: RESIDUES (NH2) AND (OXE) ARE NOT MATCHED ALTHOUGH THEY COMPND 11 ARE PRESENT IN COORDINATE FILE. PLEASE CHECK. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GABARAP, FLC3B, HT004; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS AUTOPHAGY-RELATED PROTEIN, STAPLED PEPTIDE, GABARAP, INHIBITOR, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.UEFFING,H.BROWN,D.WILLBOLD,J.A.KRITZER,O.H.WEIERGRAEBER REVDAT 2 31-JAN-24 7ZKR 1 REMARK REVDAT 1 31-AUG-22 7ZKR 0 JRNL AUTH H.BROWN,M.CHUNG,A.UFFING,N.BATISTATOU,T.TSANG,S.DOSKOCIL, JRNL AUTH 2 W.MAO,D.WILLBOLD,R.C.BAST JR.,Z.LU,O.H.WEIERGRABER, JRNL AUTH 3 J.A.KRITZER JRNL TITL STRUCTURE-BASED DESIGN OF STAPLED PEPTIDES THAT BIND GABARAP JRNL TITL 2 AND INHIBIT AUTOPHAGY. JRNL REF J.AM.CHEM.SOC. V. 144 14687 2022 JRNL REFN ESSN 1520-5126 JRNL PMID 35917476 JRNL DOI 10.1021/JACS.2C04699 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 65277 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3265 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 49.5100 - 3.1300 1.00 2829 150 0.1408 0.1705 REMARK 3 2 3.1300 - 2.4800 1.00 2737 144 0.1438 0.1783 REMARK 3 3 2.4800 - 2.1700 1.00 2729 143 0.1379 0.1659 REMARK 3 4 2.1700 - 1.9700 1.00 2701 142 0.1288 0.1350 REMARK 3 5 1.9700 - 1.8300 1.00 2704 143 0.1315 0.1526 REMARK 3 6 1.8300 - 1.7200 1.00 2708 142 0.1316 0.1659 REMARK 3 7 1.7200 - 1.6400 1.00 2706 143 0.1160 0.1269 REMARK 3 8 1.6400 - 1.5600 1.00 2668 140 0.1080 0.1478 REMARK 3 9 1.5600 - 1.5000 1.00 2699 142 0.1130 0.1359 REMARK 3 10 1.5000 - 1.4500 1.00 2701 142 0.1154 0.1523 REMARK 3 11 1.4500 - 1.4100 1.00 2687 142 0.1197 0.1541 REMARK 3 12 1.4100 - 1.3700 1.00 2685 141 0.1311 0.1662 REMARK 3 13 1.3700 - 1.3300 1.00 2694 142 0.1298 0.1674 REMARK 3 14 1.3300 - 1.3000 1.00 2663 140 0.1400 0.1775 REMARK 3 15 1.3000 - 1.2700 1.00 2690 142 0.1439 0.1584 REMARK 3 16 1.2700 - 1.2400 1.00 2688 141 0.1696 0.2214 REMARK 3 17 1.2400 - 1.2200 1.00 2649 139 0.1624 0.2008 REMARK 3 18 1.2200 - 1.1900 1.00 2686 142 0.1457 0.1721 REMARK 3 19 1.1900 - 1.1700 1.00 2677 141 0.1651 0.1716 REMARK 3 20 1.1700 - 1.1500 1.00 2696 142 0.1710 0.1796 REMARK 3 21 1.1500 - 1.1300 1.00 2672 140 0.1884 0.2360 REMARK 3 22 1.1300 - 1.1200 1.00 2686 142 0.2951 0.3040 REMARK 3 23 1.1200 - 1.1000 1.00 2657 140 0.3507 0.3913 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) : 0.112 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.849 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.32 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 : 0.005 1375 REMARK 3 ANGLE : 0.790 1881 REMARK 3 CHIRALITY : 0.086 187 REMARK 3 PLANARITY : 0.012 248 REMARK 3 DIHEDRAL : 12.754 524 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ZKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65281 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 70.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 17.77 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 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 FOR SHELL : 1.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3D32 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM ACETATE, SODIUM CACODYLATE, REMARK 280 PEG 8000, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 49.51500 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 49.51500 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 49.51500 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 49.51500 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 49.51500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 49.51500 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 49.51500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 49.51500 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 49.51500 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 49.51500 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 49.51500 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 49.51500 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 49.51500 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 49.51500 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 49.51500 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 49.51500 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 49.51500 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 49.51500 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 49.51500 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 49.51500 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 49.51500 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 49.51500 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 49.51500 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 49.51500 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 49.51500 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 49.51500 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, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL B 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 209 LIES ON A SPECIAL POSITION. 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY A 116 REMARK 465 LEU A 117 REMARK 465 ACE B 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 2 CD CE NZ REMARK 470 LYS A 13 CE NZ REMARK 470 LYS A 38 CE NZ REMARK 470 LYS A 66 CE NZ 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 38 3.22 82.00 REMARK 500 ARG A 40 51.22 -105.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 28 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 484 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 485 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 486 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 487 DISTANCE = 7.23 ANGSTROMS DBREF 7ZKR A 1 117 UNP O95166 GBRAP_HUMAN 1 117 DBREF 7ZKR B 0 13 PDB 7ZKR 7ZKR 0 13 SEQADV 7ZKR GLY A -1 UNP O95166 EXPRESSION TAG SEQADV 7ZKR SER A 0 UNP O95166 EXPRESSION TAG SEQRES 1 A 119 GLY SER MET LYS PHE VAL TYR LYS GLU GLU HIS PRO PHE SEQRES 2 A 119 GLU LYS ARG ARG SER GLU GLY GLU LYS ILE ARG LYS LYS SEQRES 3 A 119 TYR PRO ASP ARG VAL PRO VAL ILE VAL GLU LYS ALA PRO SEQRES 4 A 119 LYS ALA ARG ILE GLY ASP LEU ASP LYS LYS LYS TYR LEU SEQRES 5 A 119 VAL PRO SER ASP LEU THR VAL GLY GLN PHE TYR PHE LEU SEQRES 6 A 119 ILE ARG LYS ARG ILE HIS LEU ARG ALA GLU ASP ALA LEU SEQRES 7 A 119 PHE PHE PHE VAL ASN ASN VAL ILE PRO PRO THR SER ALA SEQRES 8 A 119 THR MET GLY GLN LEU TYR GLN GLU HIS HIS GLU GLU ASP SEQRES 9 A 119 PHE PHE LEU TYR ILE ALA TYR SER ASP GLU SER VAL TYR SEQRES 10 A 119 GLY LEU SEQRES 1 B 14 ACE ASP ALA LE1 TYR THR TRP GLU CYS LEU ALA TRP PRO SEQRES 2 B 14 NH2 HET LE1 B 3 8 HET NH2 B 13 1 HET PO4 A 201 5 HET PO4 A 202 5 HET PO4 A 203 5 HET CL B 101 1 HET OXE B 102 8 HETNAM LE1 3-SULFANYL-L-VALINE HETNAM NH2 AMINO GROUP HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETNAM OXE ORTHO-XYLENE HETSYN LE1 L-LE1ICILLAMINE; L-PENICILLAMINE FORMUL 2 LE1 C5 H11 N O2 S FORMUL 2 NH2 H2 N FORMUL 3 PO4 3(O4 P 3-) FORMUL 6 CL CL 1- FORMUL 7 OXE C8 H10 FORMUL 8 HOH *206(H2 O) HELIX 1 AA1 PHE A 3 HIS A 9 1 7 HELIX 2 AA2 PRO A 10 TYR A 25 1 16 HELIX 3 AA3 THR A 56 ILE A 68 1 13 HELIX 4 AA4 THR A 90 HIS A 99 1 10 HELIX 5 AA5 TRP B 6 ALA B 10 5 5 SHEET 1 AA1 4 LYS A 48 PRO A 52 0 SHEET 2 AA1 4 ARG A 28 LYS A 35 -1 N VAL A 31 O TYR A 49 SHEET 3 AA1 4 LEU A 105 SER A 110 1 O ILE A 107 N ILE A 32 SHEET 4 AA1 4 PHE A 77 PHE A 79 -1 N PHE A 77 O SER A 110 LINK C AALA B 2 N LE1 B 3 1555 1555 1.33 LINK C BALA B 2 N LE1 B 3 1555 1555 1.33 LINK C LE1 B 3 N TYR B 4 1555 1555 1.33 LINK SG LE1 B 3 C2' OXE B 102 1555 1555 1.82 LINK SG CYS B 8 C1' OXE B 102 1555 1555 1.83 LINK C PRO B 12 N NH2 B 13 1555 1555 1.33 CRYST1 99.030 99.030 99.030 90.00 90.00 90.00 I 2 3 24 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 0.010098 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010098 0.00000