HEADER PROTEIN BINDING 14-FEB-22 7WWQ TITLE CRYSTAL STRUCTURE OF HUMAN UFD1-NPL4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR PROTEIN LOCALIZATION PROTEIN 4 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN NPL4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UBIQUITIN RECOGNITION FACTOR IN ER-ASSOCIATED DEGRADATION COMPND 8 PROTEIN 1; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: UBIQUITIN FUSION DEGRADATION PROTEIN 1,UB FUSION PROTEIN 1; COMPND 11 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: NPLOC4, KIAA1499, NPL4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UFD1, UFD1L; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS P97, UFD1, NPL4, EDOPLASMID RETICULUM-ASSOCIATED DEGRADATION, KEYWDS 2 UBIQUITIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.Q.NGUYEN,L.T.M.LE,D.H.KIM,K.S.KO,H.T.LEE,Y.T.K.NGUYEN,H.S.KIM, AUTHOR 2 B.W.HAN,W.KANG,J.K.YANG REVDAT 3 16-NOV-22 7WWQ 1 JRNL REVDAT 2 28-SEP-22 7WWQ 1 JRNL REVDAT 1 21-SEP-22 7WWQ 0 JRNL AUTH T.Q.NGUYEN,L.T.MY LE,D.H.KIM,K.S.KO,H.T.LEE,Y.T.KIM NGUYEN, JRNL AUTH 2 H.S.KIM,B.W.HAN,W.KANG,J.K.YANG JRNL TITL STRUCTURAL BASIS FOR THE INTERACTION BETWEEN HUMAN NPL4 AND JRNL TITL 2 NPL4-BINDING MOTIF OF HUMAN UFD1. JRNL REF STRUCTURE V. 30 1530 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 36087575 JRNL DOI 10.1016/J.STR.2022.08.005 REMARK 2 REMARK 2 RESOLUTION. 2.72 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 32522 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.240 REMARK 3 FREE R VALUE TEST SET COUNT : 1703 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 30.2400 - 6.2200 1.00 2711 142 0.2570 0.2697 REMARK 3 2 6.2100 - 4.9400 1.00 2647 128 0.2427 0.2619 REMARK 3 3 4.9400 - 4.3200 1.00 2598 154 0.2112 0.2467 REMARK 3 4 4.3200 - 3.9200 1.00 2562 179 0.2229 0.2787 REMARK 3 5 3.9200 - 3.6400 1.00 2567 141 0.2355 0.3021 REMARK 3 6 3.6400 - 3.4300 1.00 2565 154 0.2419 0.2899 REMARK 3 7 3.4300 - 3.2600 1.00 2581 140 0.2368 0.2690 REMARK 3 8 3.2600 - 3.1200 1.00 2568 147 0.2373 0.2694 REMARK 3 9 3.1200 - 3.0000 1.00 2579 137 0.2614 0.3072 REMARK 3 10 3.0000 - 2.8900 1.00 2569 131 0.2636 0.2958 REMARK 3 11 2.8900 - 2.8000 1.00 2572 133 0.2653 0.3040 REMARK 3 12 2.8000 - 2.7200 0.89 2300 117 0.2804 0.3281 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.517 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.30 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 3294 REMARK 3 ANGLE : 1.125 4466 REMARK 3 CHIRALITY : 0.059 494 REMARK 3 PLANARITY : 0.009 581 REMARK 3 DIHEDRAL : 7.279 433 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 107 THROUGH 274 ) REMARK 3 ORIGIN FOR THE GROUP (A): 109.0933 7.5005 24.9680 REMARK 3 T TENSOR REMARK 3 T11: 1.2231 T22: 0.4913 REMARK 3 T33: 0.4529 T12: -0.2538 REMARK 3 T13: 0.0213 T23: -0.1173 REMARK 3 L TENSOR REMARK 3 L11: 2.0422 L22: 2.9157 REMARK 3 L33: 2.0185 L12: 1.5930 REMARK 3 L13: 0.2350 L23: 0.6814 REMARK 3 S TENSOR REMARK 3 S11: -0.4871 S12: 0.4308 S13: -0.4960 REMARK 3 S21: -1.1864 S22: 0.4035 S23: -0.1150 REMARK 3 S31: 1.1050 S32: -0.1333 S33: -0.0327 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 466 ) REMARK 3 ORIGIN FOR THE GROUP (A): 98.6737 15.0367 27.5114 REMARK 3 T TENSOR REMARK 3 T11: 0.8413 T22: 0.4628 REMARK 3 T33: 0.5799 T12: -0.4218 REMARK 3 T13: -0.3592 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.5741 L22: 3.8217 REMARK 3 L33: 2.1452 L12: -0.4293 REMARK 3 L13: -0.0223 L23: -0.0906 REMARK 3 S TENSOR REMARK 3 S11: -0.2437 S12: 0.2066 S13: -0.2203 REMARK 3 S21: -1.3438 S22: 0.2737 S23: 0.9574 REMARK 3 S31: 0.8968 S32: -0.4192 S33: 0.0277 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 467 THROUGH 560 ) REMARK 3 ORIGIN FOR THE GROUP (A): 126.9867 32.6041 32.9100 REMARK 3 T TENSOR REMARK 3 T11: 0.4180 T22: 0.4867 REMARK 3 T33: 0.4842 T12: -0.0618 REMARK 3 T13: 0.1474 T23: -0.0358 REMARK 3 L TENSOR REMARK 3 L11: 2.5818 L22: 3.9498 REMARK 3 L33: 2.4728 L12: 0.7141 REMARK 3 L13: -0.5579 L23: 0.2664 REMARK 3 S TENSOR REMARK 3 S11: -0.0837 S12: 0.1926 S13: 0.4172 REMARK 3 S21: -0.6160 S22: 0.2372 S23: -0.7685 REMARK 3 S31: 0.2342 S32: 0.3729 S33: -0.1274 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 258 THROUGH 262 ) REMARK 3 ORIGIN FOR THE GROUP (A): 81.0202 22.0138 26.8246 REMARK 3 T TENSOR REMARK 3 T11: 1.2413 T22: 1.2848 REMARK 3 T33: 2.0503 T12: -0.2776 REMARK 3 T13: -0.9230 T23: -0.4019 REMARK 3 L TENSOR REMARK 3 L11: 1.1866 L22: 0.7625 REMARK 3 L33: 2.7041 L12: -0.1343 REMARK 3 L13: 0.0438 L23: -1.4311 REMARK 3 S TENSOR REMARK 3 S11: 0.0417 S12: 0.0804 S13: 0.1557 REMARK 3 S21: 0.1195 S22: 0.0433 S23: -0.1458 REMARK 3 S31: -0.2559 S32: 0.7665 S33: -0.0590 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 263 THROUGH 273 ) REMARK 3 ORIGIN FOR THE GROUP (A): 90.9117 24.3482 31.4580 REMARK 3 T TENSOR REMARK 3 T11: 0.7253 T22: 0.7052 REMARK 3 T33: 0.9324 T12: -0.3379 REMARK 3 T13: -0.3566 T23: 0.1330 REMARK 3 L TENSOR REMARK 3 L11: 1.3950 L22: 2.6519 REMARK 3 L33: 4.2147 L12: -0.2808 REMARK 3 L13: 0.2185 L23: 0.3438 REMARK 3 S TENSOR REMARK 3 S11: -0.0821 S12: -0.3273 S13: 0.1532 REMARK 3 S21: -0.1673 S22: -0.5515 S23: 0.8015 REMARK 3 S31: 0.0045 S32: -0.7530 S33: 0.2304 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 7WWQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32527 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 16.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 40.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 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) : 0.48600 REMARK 200 FOR SHELL : 6.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH8.5), 5 % (V/V) REMARK 280 GLYCEROL, AND 1.3 M MAGNESIUM SULFATE HYDRATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 2 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 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 82.71200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 96.43850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 82.71200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 96.43850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 82.71200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 96.43850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 82.71200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 96.43850 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 76.47900 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 96.43850 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 76.47900 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 96.43850 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 76.47900 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 96.43850 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 76.47900 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 96.43850 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 76.47900 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 82.71200 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 76.47900 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 82.71200 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 76.47900 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 82.71200 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 76.47900 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 82.71200 REMARK 290 SMTRY3 16 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 GLY A 96 REMARK 465 PHE A 97 REMARK 465 LYS A 98 REMARK 465 VAL A 99 REMARK 465 PHE A 100 REMARK 465 GLY A 101 REMARK 465 ALA A 102 REMARK 465 PRO A 103 REMARK 465 ASN A 104 REMARK 465 VAL A 105 REMARK 465 VAL A 106 REMARK 465 TYR A 122 REMARK 465 ARG A 123 REMARK 465 SER A 124 REMARK 465 ARG A 125 REMARK 465 ASP A 126 REMARK 465 PRO A 127 REMARK 465 GLN A 128 REMARK 465 LEU A 129 REMARK 465 CYS A 130 REMARK 465 ARG A 131 REMARK 465 HIS A 132 REMARK 465 GLY A 133 REMARK 465 PRO A 134 REMARK 465 LEU A 135 REMARK 465 GLY A 136 REMARK 465 LYS A 137 REMARK 465 CYS A 138 REMARK 465 VAL A 139 REMARK 465 HIS A 140 REMARK 465 CYS A 141 REMARK 465 VAL A 142 REMARK 465 PRO A 143 REMARK 465 LEU A 144 REMARK 465 GLU A 145 REMARK 465 PRO A 146 REMARK 465 PHE A 147 REMARK 465 GLY A 174 REMARK 465 ALA A 175 REMARK 465 ASP A 176 REMARK 465 LYS A 177 REMARK 465 GLY A 178 REMARK 465 LYS A 179 REMARK 465 PHE A 180 REMARK 465 VAL A 181 REMARK 465 ALA A 182 REMARK 465 LEU A 183 REMARK 465 GLU A 184 REMARK 465 ASN A 185 REMARK 465 LYS A 189 REMARK 465 ILE A 190 REMARK 465 LYS A 191 REMARK 465 SER A 192 REMARK 465 GLY A 193 REMARK 465 CYS A 194 REMARK 465 GLU A 195 REMARK 465 GLY A 196 REMARK 465 HIS A 197 REMARK 465 LEU A 198 REMARK 465 PRO A 199 REMARK 465 TRP A 200 REMARK 465 PRO A 201 REMARK 465 ASN A 202 REMARK 465 GLY A 203 REMARK 465 ILE A 204 REMARK 465 CYS A 205 REMARK 465 THR A 206 REMARK 465 LYS A 207 REMARK 465 CYS A 208 REMARK 465 GLN A 209 REMARK 465 PRO A 210 REMARK 465 SER A 211 REMARK 465 ALA A 212 REMARK 465 SER A 415 REMARK 465 SER A 416 REMARK 465 SER A 417 REMARK 465 GLU A 418 REMARK 465 GLN A 419 REMARK 465 TYR A 420 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 ASP A 148 CG OD1 OD2 REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 LEU A 152 CG CD1 CD2 REMARK 470 HIS A 154 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 155 CG CD1 CD2 REMARK 470 GLU A 156 CG CD OE1 OE2 REMARK 470 ASP A 360 CG OD1 OD2 REMARK 470 GLN A 522 CG CD OE1 NE2 REMARK 470 ILE A 525 CG1 CG2 CD1 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 NH2 ARG A 321 O HOH A 601 2.07 REMARK 500 OE1 GLN A 548 O HOH A 602 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 430 NE2 GLN A 438 2655 2.05 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 120 -157.72 -120.76 REMARK 500 HIS A 154 -58.67 -137.37 REMARK 500 PRO A 157 158.02 -43.08 REMARK 500 THR A 172 52.58 -103.85 REMARK 500 THR A 333 -105.29 -125.10 REMARK 500 PRO A 359 33.37 -64.61 REMARK 500 ASP A 360 -12.59 -143.51 REMARK 500 TYR A 411 131.35 -170.24 REMARK 500 PRO A 422 -170.95 -66.65 REMARK 500 ASP A 430 -158.16 -92.37 REMARK 500 LEU A 439 131.57 -33.70 REMARK 500 ASN B 260 -71.15 -116.62 REMARK 500 GLU B 262 79.58 -168.29 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 VAL A 421 PRO A 422 -149.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 7WWQ A 96 560 UNP Q8TAT6 NPL4_HUMAN 96 560 DBREF 7WWQ B 258 273 UNP Q92890 UFD1_HUMAN 258 273 SEQRES 1 A 465 GLY PHE LYS VAL PHE GLY ALA PRO ASN VAL VAL GLU ASP SEQRES 2 A 465 GLU ILE ASP GLN TYR LEU SER LYS GLN ASP GLY LYS ILE SEQRES 3 A 465 TYR ARG SER ARG ASP PRO GLN LEU CYS ARG HIS GLY PRO SEQRES 4 A 465 LEU GLY LYS CYS VAL HIS CYS VAL PRO LEU GLU PRO PHE SEQRES 5 A 465 ASP GLU ASP TYR LEU ASN HIS LEU GLU PRO PRO VAL LYS SEQRES 6 A 465 HIS MET SER PHE HIS ALA TYR ILE ARG LYS LEU THR GLY SEQRES 7 A 465 GLY ALA ASP LYS GLY LYS PHE VAL ALA LEU GLU ASN ILE SEQRES 8 A 465 SER CYS LYS ILE LYS SER GLY CYS GLU GLY HIS LEU PRO SEQRES 9 A 465 TRP PRO ASN GLY ILE CYS THR LYS CYS GLN PRO SER ALA SEQRES 10 A 465 ILE THR LEU ASN ARG GLN LYS TYR ARG HIS VAL ASP ASN SEQRES 11 A 465 ILE MET PHE GLU ASN HIS THR VAL ALA ASP ARG PHE LEU SEQRES 12 A 465 ASP PHE TRP ARG LYS THR GLY ASN GLN HIS PHE GLY TYR SEQRES 13 A 465 LEU TYR GLY ARG TYR THR GLU HIS LYS ASP ILE PRO LEU SEQRES 14 A 465 GLY ILE ARG ALA GLU VAL ALA ALA ILE TYR GLU PRO PRO SEQRES 15 A 465 GLN ILE GLY THR GLN ASN SER LEU GLU LEU LEU GLU ASP SEQRES 16 A 465 PRO LYS ALA GLU VAL VAL ASP GLU ILE ALA ALA LYS LEU SEQRES 17 A 465 GLY LEU ARG LYS VAL GLY TRP ILE PHE THR ASP LEU VAL SEQRES 18 A 465 SER GLU ASP THR ARG LYS GLY THR VAL ARG TYR SER ARG SEQRES 19 A 465 ASN LYS ASP THR TYR PHE LEU SER SER GLU GLU CYS ILE SEQRES 20 A 465 THR ALA GLY ASP PHE GLN ASN LYS HIS PRO ASN MET CYS SEQRES 21 A 465 ARG LEU SER PRO ASP GLY HIS PHE GLY SER LYS PHE VAL SEQRES 22 A 465 THR ALA VAL ALA THR GLY GLY PRO ASP ASN GLN VAL HIS SEQRES 23 A 465 PHE GLU GLY TYR GLN VAL SER ASN GLN CYS MET ALA LEU SEQRES 24 A 465 VAL ARG ASP GLU CYS LEU LEU PRO CYS LYS ASP ALA PRO SEQRES 25 A 465 GLU LEU GLY TYR ALA LYS GLU SER SER SER GLU GLN TYR SEQRES 26 A 465 VAL PRO ASP VAL PHE TYR LYS ASP VAL ASP LYS PHE GLY SEQRES 27 A 465 ASN GLU ILE THR GLN LEU ALA ARG PRO LEU PRO VAL GLU SEQRES 28 A 465 TYR LEU ILE ILE ASP ILE THR THR THR PHE PRO LYS ASP SEQRES 29 A 465 PRO VAL TYR THR PHE SER ILE SER GLN ASN PRO PHE PRO SEQRES 30 A 465 ILE GLU ASN ARG ASP VAL LEU GLY GLU THR GLN ASP PHE SEQRES 31 A 465 HIS SER LEU ALA THR TYR LEU SER GLN ASN THR SER SER SEQRES 32 A 465 VAL PHE LEU ASP THR ILE SER ASP PHE HIS LEU LEU LEU SEQRES 33 A 465 PHE LEU VAL THR ASN GLU VAL MET PRO LEU GLN ASP SER SEQRES 34 A 465 ILE SER LEU LEU LEU GLU ALA VAL ARG THR ARG ASN GLU SEQRES 35 A 465 GLU LEU ALA GLN THR TRP LYS ARG SER GLU GLN TRP ALA SEQRES 36 A 465 THR ILE GLU GLN LEU CYS SER THR VAL GLY SEQRES 1 B 16 ILE PRO ASN TYR GLU PHE LYS LEU GLY LYS ILE THR PHE SEQRES 2 B 16 ILE ARG ASN FORMUL 3 HOH *51(H2 O) HELIX 1 AA1 ASP A 108 SER A 115 1 8 HELIX 2 AA2 ASP A 150 HIS A 154 5 5 HELIX 3 AA3 PHE A 164 LYS A 170 1 7 HELIX 4 AA4 ASN A 230 GLY A 245 1 16 HELIX 5 AA5 LYS A 292 LEU A 303 1 12 HELIX 6 AA6 SER A 337 HIS A 351 1 15 HELIX 7 AA7 SER A 388 ASP A 397 1 10 HELIX 8 AA8 ARG A 476 GLY A 480 5 5 HELIX 9 AA9 ASP A 484 ASN A 495 1 12 HELIX 10 AB1 VAL A 499 SER A 505 1 7 HELIX 11 AB2 ASP A 506 ASN A 516 1 11 HELIX 12 AB3 ILE A 525 THR A 534 1 10 HELIX 13 AB4 ASN A 536 ARG A 545 1 10 HELIX 14 AB5 SER A 546 SER A 557 1 12 SHEET 1 AA1 2 MET A 162 SER A 163 0 SHEET 2 AA1 2 TYR A 220 ARG A 221 1 O ARG A 221 N MET A 162 SHEET 1 AA2 8 ASN A 225 PHE A 228 0 SHEET 2 AA2 8 GLY A 265 TYR A 274 1 O ALA A 268 N MET A 227 SHEET 3 AA2 8 PHE A 249 HIS A 259 -1 N THR A 257 O ARG A 267 SHEET 4 AA2 8 ARG A 306 THR A 313 -1 O GLY A 309 N LEU A 252 SHEET 5 AA2 8 VAL A 368 GLY A 374 1 O VAL A 368 N TRP A 310 SHEET 6 AA2 8 VAL A 380 VAL A 387 -1 O TYR A 385 N THR A 369 SHEET 7 AA2 8 ILE A 449 THR A 455 -1 O ILE A 450 N GLN A 386 SHEET 8 AA2 8 ASN A 225 PHE A 228 1 N ILE A 226 O THR A 453 SHEET 1 AA3 3 GLN A 278 THR A 281 0 SHEET 2 AA3 3 SER A 284 LEU A 287 -1 O SER A 284 N THR A 281 SHEET 3 AA3 3 LYS B 267 THR B 269 -1 O ILE B 268 N LEU A 285 SHEET 1 AA4 2 PRO A 352 MET A 354 0 SHEET 2 AA4 2 HIS A 362 SER A 365 -1 O GLY A 364 N ASN A 353 SHEET 1 AA5 3 LEU A 400 LEU A 401 0 SHEET 2 AA5 3 LEU A 409 ALA A 412 -1 O TYR A 411 N LEU A 401 SHEET 3 AA5 3 LEU A 443 PRO A 444 -1 O LEU A 443 N GLY A 410 SHEET 1 AA6 2 PHE A 425 TYR A 426 0 SHEET 2 AA6 2 GLN A 438 LEU A 439 -1 O GLN A 438 N TYR A 426 CISPEP 1 GLU A 156 PRO A 157 0 14.27 CISPEP 2 ARG A 441 PRO A 442 0 17.11 CRYST1 152.958 165.424 192.877 90.00 90.00 90.00 F 2 2 2 16 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 0.006538 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005185 0.00000