HEADER PROTEIN BINDING 20-APR-19 6JWH TITLE YEAST NPL4 ZINC FINGER, MPN AND CTD DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR PROTEIN LOCALIZATION PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HMG-COA REDUCTASE DEGRADATION PROTEIN 4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 GENE: NPL4, HRD4, YBR170C, YBR1231; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS UBIQUITIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.SATO,S.FUKAI REVDAT 2 27-MAR-24 6JWH 1 REMARK REVDAT 1 25-DEC-19 6JWH 0 JRNL AUTH Y.SATO,H.TSUCHIYA,A.YAMAGATA,K.OKATSU,K.TANAKA,Y.SAEKI, JRNL AUTH 2 S.FUKAI JRNL TITL STRUCTURAL INSIGHTS INTO UBIQUITIN RECOGNITION AND UFD1 JRNL TITL 2 INTERACTION OF NPL4. JRNL REF NAT COMMUN V. 10 5708 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31836717 JRNL DOI 10.1038/S41467-019-13697-Y REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.349 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 58133 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.947 REMARK 3 FREE R VALUE TEST SET COUNT : 2876 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 47.8651 - 4.7439 0.99 3007 169 0.1619 0.1749 REMARK 3 2 4.7439 - 3.7658 1.00 2877 168 0.1315 0.1684 REMARK 3 3 3.7658 - 3.2899 0.99 2855 147 0.1472 0.1530 REMARK 3 4 3.2899 - 2.9892 0.99 2859 131 0.1615 0.1909 REMARK 3 5 2.9892 - 2.7750 0.99 2816 151 0.1665 0.2098 REMARK 3 6 2.7750 - 2.6114 0.99 2774 156 0.1688 0.2051 REMARK 3 7 2.6114 - 2.4806 0.98 2754 152 0.1711 0.2167 REMARK 3 8 2.4806 - 2.3726 0.99 2762 153 0.1711 0.2443 REMARK 3 9 2.3726 - 2.2813 0.98 2765 159 0.1725 0.2213 REMARK 3 10 2.2813 - 2.2026 0.98 2752 129 0.1704 0.1921 REMARK 3 11 2.2026 - 2.1337 0.98 2765 133 0.1661 0.2114 REMARK 3 12 2.1337 - 2.0727 0.98 2738 147 0.1642 0.1830 REMARK 3 13 2.0727 - 2.0181 0.97 2718 144 0.1663 0.2064 REMARK 3 14 2.0181 - 1.9689 0.96 2708 133 0.1816 0.2273 REMARK 3 15 1.9689 - 1.9241 0.96 2688 147 0.2011 0.2246 REMARK 3 16 1.9241 - 1.8832 0.95 2665 121 0.2018 0.2268 REMARK 3 17 1.8832 - 1.8455 0.91 2520 120 0.2062 0.2404 REMARK 3 18 1.8455 - 1.8107 0.85 2367 126 0.2167 0.3069 REMARK 3 19 1.8107 - 1.7783 0.77 2174 100 0.2232 0.2385 REMARK 3 20 1.7783 - 1.7482 0.72 2001 97 0.2452 0.2683 REMARK 3 21 1.7482 - 1.7200 0.61 1692 93 0.2952 0.3615 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) : 0.178 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.424 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.07 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 : 0.010 3853 REMARK 3 ANGLE : 1.198 5201 REMARK 3 CHIRALITY : 0.061 549 REMARK 3 PLANARITY : 0.006 671 REMARK 3 DIHEDRAL : 14.576 1439 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 43.9826 28.5329 49.2051 REMARK 3 T TENSOR REMARK 3 T11: 0.1414 T22: 0.1495 REMARK 3 T33: 0.1538 T12: -0.0053 REMARK 3 T13: -0.0220 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.9717 L22: 1.7094 REMARK 3 L33: 1.1931 L12: -0.2973 REMARK 3 L13: -0.0866 L23: 0.4574 REMARK 3 S TENSOR REMARK 3 S11: 0.0590 S12: 0.1004 S13: -0.0919 REMARK 3 S21: -0.0096 S22: -0.1106 S23: -0.0427 REMARK 3 S31: -0.0371 S32: 0.0087 S33: 0.0354 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 6JWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300011917. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-17 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28260 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62488 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 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 (%) : 96.6 REMARK 200 DATA REDUNDANCY : 15.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43100 REMARK 200 FOR SHELL : 2.060 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% TACSIMAT (PH 6.0), 12% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 37.98550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.06150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.46800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.06150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.98550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.46800 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL 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 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 108 REMARK 465 PRO A 109 REMARK 465 LEU A 110 REMARK 465 GLY A 111 REMARK 465 SER A 112 REMARK 465 LYS A 182 REMARK 465 LYS A 183 REMARK 465 GLU A 184 REMARK 465 ASN A 185 REMARK 465 GLY A 186 REMARK 465 SER A 187 REMARK 465 SER A 188 REMARK 465 TYR A 189 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 O HOH A 796 O HOH A 1051 2.02 REMARK 500 O HOH A 712 O HOH A 923 2.03 REMARK 500 O3 GOL A 611 O HOH A 701 2.18 REMARK 500 O HOH A 1029 O HOH A 1062 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 SER A 347 -96.27 -132.32 REMARK 500 SER A 378 -139.53 50.86 REMARK 500 SER A 417 -141.32 -140.98 REMARK 500 ASP A 460 -39.69 -39.36 REMARK 500 GLU A 476 109.47 -59.57 REMARK 500 ASN A 526 114.38 -161.10 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 TYR A 399 GLN A 400 150.00 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 A1106 DISTANCE = 7.13 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 137 SG REMARK 620 2 HIS A 139 NE2 113.5 REMARK 620 3 CYS A 145 SG 107.7 106.2 REMARK 620 4 CYS A 148 SG 109.6 100.3 119.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 204 SG REMARK 620 2 HIS A 208 NE2 105.7 REMARK 620 3 CYS A 216 SG 111.5 107.0 REMARK 620 4 CYS A 219 SG 112.1 105.2 114.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 611 DBREF 6JWH A 113 580 UNP P33755 NPL4_YEAST 113 580 SEQADV 6JWH GLY A 108 UNP P33755 EXPRESSION TAG SEQADV 6JWH PRO A 109 UNP P33755 EXPRESSION TAG SEQADV 6JWH LEU A 110 UNP P33755 EXPRESSION TAG SEQADV 6JWH GLY A 111 UNP P33755 EXPRESSION TAG SEQADV 6JWH SER A 112 UNP P33755 EXPRESSION TAG SEQADV 6JWH ALA A 123 UNP P33755 GLU 123 ENGINEERED MUTATION SEQADV 6JWH ALA A 124 UNP P33755 LYS 124 ENGINEERED MUTATION SEQADV 6JWH ALA A 125 UNP P33755 GLU 125 ENGINEERED MUTATION SEQRES 1 A 473 GLY PRO LEU GLY SER ILE LYS GLU LEU ALA VAL ASP GLU SEQRES 2 A 473 GLU LEU ALA ALA ALA ASP GLY LEU ILE PRO ARG GLN LYS SEQRES 3 A 473 SER LYS LEU CYS LYS HIS GLY ASP ARG GLY MET CYS GLU SEQRES 4 A 473 TYR CYS SER PRO LEU PRO PRO TRP ASP LYS GLU TYR HIS SEQRES 5 A 473 GLU LYS ASN LYS ILE LYS HIS ILE SER PHE HIS SER TYR SEQRES 6 A 473 LEU LYS LYS LEU ASN GLU ASN ALA ASN LYS LYS GLU ASN SEQRES 7 A 473 GLY SER SER TYR ILE SER PRO LEU SER GLU PRO ASP PHE SEQRES 8 A 473 ARG ILE ASN LYS ARG CYS HIS ASN GLY HIS GLU PRO TRP SEQRES 9 A 473 PRO ARG GLY ILE CYS SER LYS CYS GLN PRO SER ALA ILE SEQRES 10 A 473 THR LEU GLN GLN GLN GLU PHE ARG MET VAL ASP HIS VAL SEQRES 11 A 473 GLU PHE GLN LYS SER GLU ILE ILE ASN GLU PHE ILE GLN SEQRES 12 A 473 ALA TRP ARG TYR THR GLY MET GLN ARG PHE GLY TYR MET SEQRES 13 A 473 TYR GLY SER TYR SER LYS TYR ASP ASN THR PRO LEU GLY SEQRES 14 A 473 ILE LYS ALA VAL VAL GLU ALA ILE TYR GLU PRO PRO GLN SEQRES 15 A 473 HIS ASP GLU GLN ASP GLY LEU THR MET ASP VAL GLU GLN SEQRES 16 A 473 VAL LYS ASN GLU MET LEU GLN ILE ASP ARG GLN ALA GLN SEQRES 17 A 473 GLU MET GLY LEU SER ARG ILE GLY LEU ILE PHE THR ASP SEQRES 18 A 473 LEU SER ASP ALA GLY ALA GLY ASP GLY SER VAL PHE CYS SEQRES 19 A 473 LYS ARG HIS LYS ASP SER PHE PHE LEU SER SER LEU GLU SEQRES 20 A 473 VAL ILE MET ALA ALA ARG HIS GLN THR ARG HIS PRO ASN SEQRES 21 A 473 VAL SER LYS TYR SER GLU GLN GLY PHE PHE SER SER LYS SEQRES 22 A 473 PHE VAL THR CYS VAL ILE SER GLY ASN LEU GLU GLY GLU SEQRES 23 A 473 ILE ASP ILE SER SER TYR GLN VAL SER THR GLU ALA GLU SEQRES 24 A 473 ALA LEU VAL THR ALA ASP MET ILE SER GLY SER THR PHE SEQRES 25 A 473 PRO SER MET ALA TYR ILE ASN ASP THR THR ASP GLU ARG SEQRES 26 A 473 TYR VAL PRO GLU ILE PHE TYR MET LYS SER ASN GLU TYR SEQRES 27 A 473 GLY ILE THR VAL LYS GLU ASN ALA LYS PRO ALA PHE PRO SEQRES 28 A 473 VAL ASP TYR LEU LEU VAL THR LEU THR HIS GLY PHE PRO SEQRES 29 A 473 ASN THR ASP THR GLU THR ASN SER LYS PHE VAL SER SER SEQRES 30 A 473 THR GLY PHE PRO TRP SER ASN ARG GLN ALA MET GLY GLN SEQRES 31 A 473 SER GLN ASP TYR GLN GLU LEU LYS LYS TYR LEU PHE ASN SEQRES 32 A 473 VAL ALA SER SER GLY ASP PHE ASN LEU LEU HIS GLU LYS SEQRES 33 A 473 ILE SER ASN PHE HIS LEU LEU LEU TYR ILE ASN SER LEU SEQRES 34 A 473 GLN ILE LEU SER PRO ASP GLU TRP LYS LEU LEU ILE GLU SEQRES 35 A 473 SER ALA VAL LYS ASN GLU TRP GLU GLU SER LEU LEU LYS SEQRES 36 A 473 LEU VAL SER SER ALA GLY TRP GLN THR LEU VAL MET ILE SEQRES 37 A 473 LEU GLN GLU SER GLY HET ZN A 601 1 HET ZN A 602 1 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET GOL A 606 6 HET GOL A 607 6 HET GOL A 608 6 HET GOL A 609 6 HET GOL A 610 6 HET GOL A 611 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 GOL 9(C3 H8 O3) FORMUL 13 HOH *406(H2 O) HELIX 1 AA1 LEU A 116 ALA A 124 1 9 HELIX 2 AA2 ASP A 155 ASN A 162 1 8 HELIX 3 AA3 PHE A 169 ALA A 180 1 12 HELIX 4 AA4 LYS A 241 GLY A 256 1 16 HELIX 5 AA5 ASP A 299 MET A 317 1 19 HELIX 6 AA6 SER A 351 HIS A 365 1 15 HELIX 7 AA7 SER A 402 ALA A 411 1 10 HELIX 8 AA8 ARG A 492 GLY A 496 5 5 HELIX 9 AA9 ASP A 500 SER A 513 1 14 HELIX 10 AB1 ASP A 516 SER A 525 1 10 HELIX 11 AB2 ASN A 526 GLN A 537 1 12 HELIX 12 AB3 SER A 540 LYS A 553 1 14 HELIX 13 AB4 TRP A 556 SER A 566 1 11 HELIX 14 AB5 SER A 566 SER A 579 1 14 SHEET 1 AA1 2 ILE A 167 SER A 168 0 SHEET 2 AA1 2 PHE A 231 ARG A 232 1 O ARG A 232 N ILE A 167 SHEET 1 AA2 3 ILE A 224 LEU A 226 0 SHEET 2 AA2 3 ILE A 437 SER A 442 1 O PHE A 438 N ILE A 224 SHEET 3 AA2 3 THR A 448 ASN A 452 -1 O GLU A 451 N TYR A 439 SHEET 1 AA3 8 HIS A 236 PHE A 239 0 SHEET 2 AA3 8 GLY A 276 TYR A 285 1 O ALA A 279 N GLU A 238 SHEET 3 AA3 8 PHE A 260 TYR A 270 -1 N SER A 266 O VAL A 280 SHEET 4 AA3 8 SER A 320 ASP A 328 -1 O ILE A 325 N GLY A 261 SHEET 5 AA3 8 VAL A 382 GLY A 388 1 O ILE A 386 N ASP A 328 SHEET 6 AA3 8 ILE A 394 VAL A 401 -1 O SER A 397 N VAL A 385 SHEET 7 AA3 8 LEU A 463 GLY A 469 -1 O LEU A 466 N SER A 398 SHEET 8 AA3 8 HIS A 236 PHE A 239 1 N PHE A 239 O GLY A 469 SHEET 1 AA4 2 HIS A 290 GLU A 292 0 SHEET 2 AA4 2 GLY A 295 THR A 297 -1 O THR A 297 N HIS A 290 SHEET 1 AA5 2 PRO A 366 VAL A 368 0 SHEET 2 AA5 2 PHE A 376 SER A 379 -1 O PHE A 377 N ASN A 367 SHEET 1 AA6 3 ILE A 414 GLY A 416 0 SHEET 2 AA6 3 MET A 422 ILE A 425 -1 O TYR A 424 N SER A 415 SHEET 3 AA6 3 ALA A 456 PRO A 458 -1 O PHE A 457 N ALA A 423 LINK SG CYS A 137 ZN ZN A 601 1555 1555 2.31 LINK NE2 HIS A 139 ZN ZN A 601 1555 1555 2.10 LINK SG CYS A 145 ZN ZN A 601 1555 1555 2.34 LINK SG CYS A 148 ZN ZN A 601 1555 1555 2.32 LINK SG CYS A 204 ZN ZN A 602 1555 1555 2.35 LINK NE2 HIS A 208 ZN ZN A 602 1555 1555 2.09 LINK SG CYS A 216 ZN ZN A 602 1555 1555 2.31 LINK SG CYS A 219 ZN ZN A 602 1555 1555 2.28 CISPEP 1 TRP A 211 PRO A 212 0 6.82 CISPEP 2 LYS A 454 PRO A 455 0 1.76 SITE 1 AC1 4 CYS A 137 HIS A 139 CYS A 145 CYS A 148 SITE 1 AC2 4 CYS A 204 HIS A 208 CYS A 216 CYS A 219 SITE 1 AC3 5 ARG A 321 HIS A 361 ARG A 364 HIS A 365 SITE 2 AC3 5 HOH A 799 SITE 1 AC4 4 GLN A 228 ASP A 460 TYR A 461 HOH A 723 SITE 1 AC5 7 GLY A 127 TYR A 158 ASP A 271 THR A 273 SITE 2 AC5 7 PRO A 274 HOH A 743 HOH A 895 SITE 1 AC6 4 GLU A 238 TYR A 270 ASP A 271 LYS A 278 SITE 1 AC7 9 GLU A 247 THR A 485 GLY A 486 PHE A 487 SITE 2 AC7 9 PRO A 488 TRP A 489 ARG A 492 GLN A 497 SITE 3 AC7 9 HOH A 734 SITE 1 AC8 6 ALA A 123 HIS A 170 LEU A 173 LYS A 174 SITE 2 AC8 6 ASN A 177 HOH A 767 SITE 1 AC9 6 PHE A 260 PHE A 326 GLU A 354 HOH A 778 SITE 2 AC9 6 HOH A 818 HOH A1051 SITE 1 AD1 5 PHE A 349 ASP A 460 THR A 465 HOH A 740 SITE 2 AD1 5 HOH A 749 SITE 1 AD2 6 SER A 320 ARG A 321 HIS A 365 HOH A 701 SITE 2 AD2 6 HOH A 708 HOH A 900 CRYST1 75.971 82.936 92.123 90.00 90.00 90.00 P 21 21 21 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 0.013163 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010855 0.00000