HEADER HYDROLASE 14-MAR-21 7NUU TITLE CRYSTAL STRUCTURE OF HUMAN AMDHD2 IN COMPLEX WITH ZN COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GLCNAC 6-P DEACETYLASE,AMIDOHYDROLASE DOMAIN-CONTAINING COMPND 5 PROTEIN 2; COMPND 6 EC: 3.5.1.25; COMPND 7 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: AMDHD2, CGI-14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE, NAGA, AMIDOHYDROLASE KEYWDS 2 DOMAIN-CONTAINING PROTEIN 2, AMDHD2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.RUEGENBERG,V.KROEF,U.BAUMANN,M.S.DENZEL REVDAT 4 31-JAN-24 7NUU 1 JRNL REVDAT 3 16-MAR-22 7NUU 1 JRNL REVDAT 2 05-MAY-21 7NUU 1 JRNL REVDAT 1 28-APR-21 7NUU 0 JRNL AUTH V.KROEF,S.RUEGENBERG,M.HORN,K.ALLMEROTH,L.EBERT,S.BOZKUS, JRNL AUTH 2 S.MIETHE,U.ELLING,B.SCHERMER,U.BAUMANN,M.S.DENZEL JRNL TITL GFPT2/GFAT2 AND AMDHD2 ACT IN TANDEM TO CONTROL THE JRNL TITL 2 HEXOSAMINE PATHWAY. JRNL REF ELIFE V. 11 2022 JRNL REFN ESSN 2050-084X JRNL PMID 35229715 JRNL DOI 10.7554/ELIFE.69223 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.KROEF,S.RUEGENBERG,M.HORN,K.ALLMEROTH,L.EBERT,S.BOZKUS, REMARK 1 AUTH 2 S.MIETHE,B.SCHERMER,U.BAUMANN,M.S.DENZEL REMARK 1 TITL GFAT2 AND AMDHD2 ACT IN TANDEM TO CONTROL THE HEXOSAMINE REMARK 1 TITL 2 BIOSYNTHETIC PATHWAY REMARK 1 REF BIORXIV 2021 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2021.04.23.441115 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 71025 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1992 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 77.0830 - 4.4255 1.00 5228 152 0.1640 0.1910 REMARK 3 2 4.4255 - 3.5126 1.00 5013 145 0.1463 0.1594 REMARK 3 3 3.5126 - 3.0686 1.00 4991 144 0.1689 0.1818 REMARK 3 4 3.0686 - 2.7880 1.00 4945 143 0.1786 0.2163 REMARK 3 5 2.7880 - 2.5882 1.00 4936 142 0.1823 0.2055 REMARK 3 6 2.5882 - 2.4355 1.00 4922 142 0.1840 0.2089 REMARK 3 7 2.4355 - 2.3136 1.00 4913 142 0.1867 0.2251 REMARK 3 8 2.3136 - 2.2128 1.00 4863 139 0.1976 0.2357 REMARK 3 9 2.2128 - 2.1277 1.00 4905 142 0.2098 0.2584 REMARK 3 10 2.1277 - 2.0542 1.00 4867 141 0.2348 0.2461 REMARK 3 11 2.0542 - 1.9900 1.00 4903 141 0.2441 0.2718 REMARK 3 12 1.9900 - 1.9331 1.00 4859 140 0.2656 0.2693 REMARK 3 13 1.9331 - 1.8822 1.00 4861 140 0.2888 0.3153 REMARK 3 14 1.8822 - 1.8363 0.99 4827 139 0.3191 0.3272 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) : 20.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.60 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 10 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.6594 -13.3730 3.6529 REMARK 3 T TENSOR REMARK 3 T11: 0.4359 T22: 0.3725 REMARK 3 T33: 0.3073 T12: -0.0803 REMARK 3 T13: -0.1058 T23: 0.0187 REMARK 3 L TENSOR REMARK 3 L11: 3.0610 L22: 2.8926 REMARK 3 L33: 8.0989 L12: 0.1523 REMARK 3 L13: 1.2426 L23: -1.4807 REMARK 3 S TENSOR REMARK 3 S11: 0.0901 S12: 0.3594 S13: 0.0099 REMARK 3 S21: -0.3736 S22: 0.1512 S23: 0.2239 REMARK 3 S31: 0.5227 S32: -0.3223 S33: -0.2463 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 57 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.2203 -11.0248 24.8875 REMARK 3 T TENSOR REMARK 3 T11: 0.2877 T22: 0.2121 REMARK 3 T33: 0.2428 T12: 0.0228 REMARK 3 T13: 0.0348 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.7628 L22: 1.5170 REMARK 3 L33: 1.6379 L12: 0.4148 REMARK 3 L13: 0.4721 L23: 0.2149 REMARK 3 S TENSOR REMARK 3 S11: -0.0295 S12: 0.1543 S13: -0.0133 REMARK 3 S21: -0.2860 S22: 0.0498 S23: -0.1694 REMARK 3 S31: 0.1646 S32: 0.2421 S33: -0.0222 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 10 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.3812 -5.6168 54.4842 REMARK 3 T TENSOR REMARK 3 T11: 0.2107 T22: 0.3263 REMARK 3 T33: 0.3517 T12: 0.0369 REMARK 3 T13: -0.0340 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 7.4888 L22: 1.8319 REMARK 3 L33: 1.4543 L12: 2.2652 REMARK 3 L13: -1.1774 L23: -0.2446 REMARK 3 S TENSOR REMARK 3 S11: 0.0430 S12: -0.1684 S13: 0.3242 REMARK 3 S21: 0.0162 S22: -0.0688 S23: 0.3248 REMARK 3 S31: -0.0376 S32: -0.1293 S33: 0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 57 THROUGH 407 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.5132 -13.7093 62.3521 REMARK 3 T TENSOR REMARK 3 T11: 0.2018 T22: 0.2452 REMARK 3 T33: 0.1699 T12: 0.0161 REMARK 3 T13: -0.0207 T23: 0.0534 REMARK 3 L TENSOR REMARK 3 L11: 2.3822 L22: 1.5687 REMARK 3 L33: 1.8202 L12: -0.7076 REMARK 3 L13: -1.0039 L23: 0.6699 REMARK 3 S TENSOR REMARK 3 S11: -0.1419 S12: -0.4740 S13: -0.1041 REMARK 3 S21: 0.2967 S22: 0.1212 S23: -0.0272 REMARK 3 S31: 0.2497 S32: 0.2696 S33: 0.0093 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 10 THROUGH 254 OR REMARK 3 (RESID 255 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 256 REMARK 3 THROUGH 405)) REMARK 3 SELECTION : (CHAIN B AND (RESID 10 THROUGH 404 OR REMARK 3 (RESID 405 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )))) REMARK 3 ATOM PAIRS NUMBER : 3598 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7NUU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292109572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MAR 15, 2019 REMARK 200 DATA SCALING SOFTWARE : XDS MAR 15, 2019 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71036 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.836 REMARK 200 RESOLUTION RANGE LOW (A) : 77.083 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.16_3549 REMARK 200 STARTING MODEL: 7NUT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS TRIS PROPANE PH 8.25, 0.25 M REMARK 280 SODIUM NITRATE, 20 % PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 30.88850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.08300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.16800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.08300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.88850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.16800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 GLY A 3 REMARK 465 GLU A 4 REMARK 465 GLN A 5 REMARK 465 GLY A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 406 REMARK 465 ALA A 407 REMARK 465 ARG A 408 REMARK 465 GLN A 409 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 GLY B 3 REMARK 465 GLU B 4 REMARK 465 GLN B 5 REMARK 465 GLY B 6 REMARK 465 ALA B 7 REMARK 465 ALA B 8 REMARK 465 GLY B 9 REMARK 465 GLN B 409 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 405 CG OD1 OD2 REMARK 470 ARG B 255 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 408 CG CD NE CZ NH1 NH2 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 O3 GOL A 502 O HOH A 601 2.03 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 ASP A 166 28.08 -140.64 REMARK 500 ALA A 167 -117.63 51.25 REMARK 500 HIS A 232 81.74 23.36 REMARK 500 PHE A 234 -24.09 80.71 REMARK 500 ASP A 244 83.28 -151.33 REMARK 500 ALA A 268 52.36 -100.08 REMARK 500 HIS A 285 72.05 -157.28 REMARK 500 SER A 358 -70.71 -150.54 REMARK 500 ASP B 166 28.55 -141.76 REMARK 500 ALA B 167 -116.74 52.47 REMARK 500 HIS B 232 82.28 24.32 REMARK 500 PHE B 234 -24.70 80.59 REMARK 500 ALA B 268 53.53 -100.70 REMARK 500 HIS B 285 71.13 -157.13 REMARK 500 SER B 358 -71.29 -150.07 REMARK 500 REMARK 500 REMARK: NULL 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 143 OE1 REMARK 620 2 HIS A 211 NE2 94.4 REMARK 620 3 HIS A 232 NE2 108.2 103.4 REMARK 620 4 GOL A 502 O2 89.7 164.7 89.3 REMARK 620 5 GOL A 502 O3 139.2 85.8 111.5 81.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 143 OE1 REMARK 620 2 HIS B 211 NE2 92.3 REMARK 620 3 HIS B 232 NE2 105.1 99.7 REMARK 620 4 GOL B 502 O1 91.4 165.2 93.1 REMARK 620 5 GOL B 502 O2 110.3 88.3 143.3 76.9 REMARK 620 N 1 2 3 4 DBREF 7NUU A 1 409 UNP Q9Y303 NAGA_HUMAN 1 409 DBREF 7NUU B 1 409 UNP Q9Y303 NAGA_HUMAN 1 409 SEQRES 1 A 409 MET ARG GLY GLU GLN GLY ALA ALA GLY ALA ARG VAL LEU SEQRES 2 A 409 GLN PHE THR ASN CYS ARG ILE LEU ARG GLY GLY LYS LEU SEQRES 3 A 409 LEU ARG GLU ASP LEU TRP VAL ARG GLY GLY ARG ILE LEU SEQRES 4 A 409 ASP PRO GLU LYS LEU PHE PHE GLU GLU ARG ARG VAL ALA SEQRES 5 A 409 ASP GLU ARG ARG ASP CYS GLY GLY ARG ILE LEU ALA PRO SEQRES 6 A 409 GLY PHE ILE ASP VAL GLN ILE ASN GLY GLY PHE GLY VAL SEQRES 7 A 409 ASP PHE SER GLN ALA THR GLU ASP VAL GLY SER GLY VAL SEQRES 8 A 409 ALA LEU VAL ALA ARG ARG ILE LEU SER HIS GLY VAL THR SEQRES 9 A 409 SER PHE CYS PRO THR LEU VAL THR SER PRO PRO GLU VAL SEQRES 10 A 409 TYR HIS LYS VAL VAL PRO GLN ILE PRO VAL LYS SER GLY SEQRES 11 A 409 GLY PRO HIS GLY ALA GLY VAL LEU GLY LEU HIS LEU GLU SEQRES 12 A 409 GLY PRO PHE ILE SER ARG GLU LYS ARG GLY ALA HIS PRO SEQRES 13 A 409 GLU ALA HIS LEU ARG SER PHE GLU ALA ASP ALA PHE GLN SEQRES 14 A 409 ASP LEU LEU ALA THR TYR GLY PRO LEU ASP ASN VAL ARG SEQRES 15 A 409 ILE VAL THR LEU ALA PRO GLU LEU GLY ARG SER HIS GLU SEQRES 16 A 409 VAL ILE ARG ALA LEU THR ALA ARG GLY ILE CYS VAL SER SEQRES 17 A 409 LEU GLY HIS SER VAL ALA ASP LEU ARG ALA ALA GLU ASP SEQRES 18 A 409 ALA VAL TRP SER GLY ALA THR PHE ILE THR HIS LEU PHE SEQRES 19 A 409 ASN ALA MET LEU PRO PHE HIS HIS ARG ASP PRO GLY ILE SEQRES 20 A 409 VAL GLY LEU LEU THR SER ASP ARG LEU PRO ALA GLY ARG SEQRES 21 A 409 CYS ILE PHE TYR GLY MET ILE ALA ASP GLY THR HIS THR SEQRES 22 A 409 ASN PRO ALA ALA LEU ARG ILE ALA HIS ARG ALA HIS PRO SEQRES 23 A 409 GLN GLY LEU VAL LEU VAL THR ASP ALA ILE PRO ALA LEU SEQRES 24 A 409 GLY LEU GLY ASN GLY ARG HIS THR LEU GLY GLN GLN GLU SEQRES 25 A 409 VAL GLU VAL ASP GLY LEU THR ALA TYR VAL ALA GLY THR SEQRES 26 A 409 LYS THR LEU SER GLY SER ILE ALA PRO MET ASP VAL CYS SEQRES 27 A 409 VAL ARG HIS PHE LEU GLN ALA THR GLY CYS SER MET GLU SEQRES 28 A 409 SER ALA LEU GLU ALA ALA SER LEU HIS PRO ALA GLN LEU SEQRES 29 A 409 LEU GLY LEU GLU LYS SER LYS GLY THR LEU ASP PHE GLY SEQRES 30 A 409 ALA ASP ALA ASP PHE VAL VAL LEU ASP ASP SER LEU HIS SEQRES 31 A 409 VAL GLN ALA THR TYR ILE SER GLY GLU LEU VAL TRP GLN SEQRES 32 A 409 ALA ASP ALA ALA ARG GLN SEQRES 1 B 409 MET ARG GLY GLU GLN GLY ALA ALA GLY ALA ARG VAL LEU SEQRES 2 B 409 GLN PHE THR ASN CYS ARG ILE LEU ARG GLY GLY LYS LEU SEQRES 3 B 409 LEU ARG GLU ASP LEU TRP VAL ARG GLY GLY ARG ILE LEU SEQRES 4 B 409 ASP PRO GLU LYS LEU PHE PHE GLU GLU ARG ARG VAL ALA SEQRES 5 B 409 ASP GLU ARG ARG ASP CYS GLY GLY ARG ILE LEU ALA PRO SEQRES 6 B 409 GLY PHE ILE ASP VAL GLN ILE ASN GLY GLY PHE GLY VAL SEQRES 7 B 409 ASP PHE SER GLN ALA THR GLU ASP VAL GLY SER GLY VAL SEQRES 8 B 409 ALA LEU VAL ALA ARG ARG ILE LEU SER HIS GLY VAL THR SEQRES 9 B 409 SER PHE CYS PRO THR LEU VAL THR SER PRO PRO GLU VAL SEQRES 10 B 409 TYR HIS LYS VAL VAL PRO GLN ILE PRO VAL LYS SER GLY SEQRES 11 B 409 GLY PRO HIS GLY ALA GLY VAL LEU GLY LEU HIS LEU GLU SEQRES 12 B 409 GLY PRO PHE ILE SER ARG GLU LYS ARG GLY ALA HIS PRO SEQRES 13 B 409 GLU ALA HIS LEU ARG SER PHE GLU ALA ASP ALA PHE GLN SEQRES 14 B 409 ASP LEU LEU ALA THR TYR GLY PRO LEU ASP ASN VAL ARG SEQRES 15 B 409 ILE VAL THR LEU ALA PRO GLU LEU GLY ARG SER HIS GLU SEQRES 16 B 409 VAL ILE ARG ALA LEU THR ALA ARG GLY ILE CYS VAL SER SEQRES 17 B 409 LEU GLY HIS SER VAL ALA ASP LEU ARG ALA ALA GLU ASP SEQRES 18 B 409 ALA VAL TRP SER GLY ALA THR PHE ILE THR HIS LEU PHE SEQRES 19 B 409 ASN ALA MET LEU PRO PHE HIS HIS ARG ASP PRO GLY ILE SEQRES 20 B 409 VAL GLY LEU LEU THR SER ASP ARG LEU PRO ALA GLY ARG SEQRES 21 B 409 CYS ILE PHE TYR GLY MET ILE ALA ASP GLY THR HIS THR SEQRES 22 B 409 ASN PRO ALA ALA LEU ARG ILE ALA HIS ARG ALA HIS PRO SEQRES 23 B 409 GLN GLY LEU VAL LEU VAL THR ASP ALA ILE PRO ALA LEU SEQRES 24 B 409 GLY LEU GLY ASN GLY ARG HIS THR LEU GLY GLN GLN GLU SEQRES 25 B 409 VAL GLU VAL ASP GLY LEU THR ALA TYR VAL ALA GLY THR SEQRES 26 B 409 LYS THR LEU SER GLY SER ILE ALA PRO MET ASP VAL CYS SEQRES 27 B 409 VAL ARG HIS PHE LEU GLN ALA THR GLY CYS SER MET GLU SEQRES 28 B 409 SER ALA LEU GLU ALA ALA SER LEU HIS PRO ALA GLN LEU SEQRES 29 B 409 LEU GLY LEU GLU LYS SER LYS GLY THR LEU ASP PHE GLY SEQRES 30 B 409 ALA ASP ALA ASP PHE VAL VAL LEU ASP ASP SER LEU HIS SEQRES 31 B 409 VAL GLN ALA THR TYR ILE SER GLY GLU LEU VAL TRP GLN SEQRES 32 B 409 ALA ASP ALA ALA ARG GLN HET ZN A 501 1 HET GOL A 502 13 HET ZN B 501 1 HET GOL B 502 13 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *318(H2 O) HELIX 1 AA1 ASP A 40 GLU A 48 1 9 HELIX 2 AA2 ASP A 86 ILE A 98 1 13 HELIX 3 AA3 LEU A 99 HIS A 101 5 3 HELIX 4 AA4 PRO A 114 VAL A 122 1 9 HELIX 5 AA5 PRO A 123 ILE A 125 5 3 HELIX 6 AA6 PRO A 156 LEU A 160 5 5 HELIX 7 AA7 ALA A 167 GLY A 176 1 10 HELIX 8 AA8 ARG A 192 ARG A 203 1 12 HELIX 9 AA9 ASP A 215 GLY A 226 1 12 HELIX 10 AB1 PRO A 245 THR A 252 5 8 HELIX 11 AB2 ASN A 274 HIS A 285 1 12 HELIX 12 AB3 PRO A 334 GLY A 347 1 14 HELIX 13 AB4 SER A 349 ALA A 357 1 9 HELIX 14 AB5 SER A 358 LEU A 365 1 8 HELIX 15 AB6 ASP B 40 GLU B 47 5 8 HELIX 16 AB7 ASP B 86 ILE B 98 1 13 HELIX 17 AB8 LEU B 99 HIS B 101 5 3 HELIX 18 AB9 PRO B 114 VAL B 122 1 9 HELIX 19 AC1 PRO B 123 ILE B 125 5 3 HELIX 20 AC2 PRO B 156 LEU B 160 5 5 HELIX 21 AC3 ALA B 167 GLY B 176 1 10 HELIX 22 AC4 ARG B 192 ARG B 203 1 12 HELIX 23 AC5 ASP B 215 GLY B 226 1 12 HELIX 24 AC6 PRO B 245 THR B 252 5 8 HELIX 25 AC7 ASN B 274 HIS B 285 1 12 HELIX 26 AC8 PRO B 334 GLY B 347 1 14 HELIX 27 AC9 SER B 349 ALA B 357 1 9 HELIX 28 AD1 SER B 358 LEU B 365 1 8 SHEET 1 AA1 4 ARG A 37 LEU A 39 0 SHEET 2 AA1 4 LEU A 31 ARG A 34 -1 N ARG A 34 O ARG A 37 SHEET 3 AA1 4 VAL A 12 THR A 16 -1 N PHE A 15 O LEU A 31 SHEET 4 AA1 4 GLU A 54 ASP A 57 1 O ARG A 56 N THR A 16 SHEET 1 AA2 6 LYS A 25 LEU A 27 0 SHEET 2 AA2 6 ARG A 19 ARG A 22 -1 N ILE A 20 O LEU A 27 SHEET 3 AA2 6 ILE A 62 PRO A 65 1 O LEU A 63 N ARG A 19 SHEET 4 AA2 6 PHE A 382 LEU A 385 -1 O LEU A 385 N ILE A 62 SHEET 5 AA2 6 VAL A 391 ILE A 396 -1 O GLN A 392 N VAL A 384 SHEET 6 AA2 6 GLU A 399 GLN A 403 -1 O TRP A 402 N THR A 394 SHEET 1 AA3 3 PHE A 67 ILE A 72 0 SHEET 2 AA3 3 VAL A 103 LEU A 110 1 O THR A 109 N ILE A 72 SHEET 3 AA3 3 GLY A 136 VAL A 137 1 O GLY A 136 N THR A 104 SHEET 1 AA4 8 PHE A 67 ILE A 72 0 SHEET 2 AA4 8 VAL A 103 LEU A 110 1 O THR A 109 N ILE A 72 SHEET 3 AA4 8 LEU A 140 GLU A 143 1 O GLU A 143 N LEU A 110 SHEET 4 AA4 8 VAL A 181 LEU A 186 1 O ARG A 182 N LEU A 140 SHEET 5 AA4 8 CYS A 206 LEU A 209 1 O SER A 208 N VAL A 184 SHEET 6 AA4 8 PHE A 229 ILE A 230 1 O PHE A 229 N LEU A 209 SHEET 7 AA4 8 PHE A 263 MET A 266 1 O GLY A 265 N ILE A 230 SHEET 8 AA4 8 LEU A 289 LEU A 291 1 O VAL A 290 N TYR A 264 SHEET 1 AA5 2 GLY A 74 GLY A 75 0 SHEET 2 AA5 2 VAL A 78 ASP A 79 -1 O VAL A 78 N GLY A 75 SHEET 1 AA6 3 GLY A 304 LEU A 308 0 SHEET 2 AA6 3 GLN A 311 ASP A 316 -1 O VAL A 313 N HIS A 306 SHEET 3 AA6 3 THR A 319 VAL A 322 -1 O THR A 319 N ASP A 316 SHEET 1 AA7 4 ARG B 37 LEU B 39 0 SHEET 2 AA7 4 LEU B 31 ARG B 34 -1 N TRP B 32 O LEU B 39 SHEET 3 AA7 4 VAL B 12 THR B 16 -1 N PHE B 15 O LEU B 31 SHEET 4 AA7 4 GLU B 54 ASP B 57 1 O ARG B 56 N GLN B 14 SHEET 1 AA8 6 LYS B 25 LEU B 27 0 SHEET 2 AA8 6 ARG B 19 ARG B 22 -1 N ARG B 22 O LYS B 25 SHEET 3 AA8 6 ILE B 62 PRO B 65 1 O LEU B 63 N ARG B 19 SHEET 4 AA8 6 PHE B 382 LEU B 385 -1 O LEU B 385 N ILE B 62 SHEET 5 AA8 6 VAL B 391 ILE B 396 -1 O TYR B 395 N PHE B 382 SHEET 6 AA8 6 GLU B 399 GLN B 403 -1 O VAL B 401 N THR B 394 SHEET 1 AA9 3 PHE B 67 ILE B 72 0 SHEET 2 AA9 3 VAL B 103 VAL B 111 1 O THR B 109 N ILE B 72 SHEET 3 AA9 3 GLY B 136 VAL B 137 1 O GLY B 136 N THR B 104 SHEET 1 AB1 8 PHE B 67 ILE B 72 0 SHEET 2 AB1 8 VAL B 103 VAL B 111 1 O THR B 109 N ILE B 72 SHEET 3 AB1 8 LEU B 140 GLU B 143 1 O GLU B 143 N LEU B 110 SHEET 4 AB1 8 VAL B 181 LEU B 186 1 O ARG B 182 N LEU B 140 SHEET 5 AB1 8 CYS B 206 LEU B 209 1 O SER B 208 N VAL B 184 SHEET 6 AB1 8 PHE B 229 ILE B 230 1 O PHE B 229 N LEU B 209 SHEET 7 AB1 8 PHE B 263 MET B 266 1 O GLY B 265 N ILE B 230 SHEET 8 AB1 8 LEU B 289 LEU B 291 1 O VAL B 290 N TYR B 264 SHEET 1 AB2 2 GLY B 74 GLY B 75 0 SHEET 2 AB2 2 VAL B 78 ASP B 79 -1 O VAL B 78 N GLY B 75 SHEET 1 AB3 3 GLY B 304 LEU B 308 0 SHEET 2 AB3 3 GLN B 311 VAL B 315 -1 O VAL B 313 N HIS B 306 SHEET 3 AB3 3 ALA B 320 VAL B 322 -1 O TYR B 321 N GLU B 314 LINK OE1 GLU A 143 ZN ZN A 501 1555 1555 1.89 LINK NE2 HIS A 211 ZN ZN A 501 1555 1555 2.00 LINK NE2 HIS A 232 ZN ZN A 501 1555 1555 2.07 LINK ZN ZN A 501 O2 GOL A 502 1555 1555 2.52 LINK ZN ZN A 501 O3 GOL A 502 1555 1555 2.29 LINK OE1 GLU B 143 ZN ZN B 501 1555 1555 1.86 LINK NE2 HIS B 211 ZN ZN B 501 1555 1555 2.04 LINK NE2 HIS B 232 ZN ZN B 501 1555 1555 2.15 LINK ZN ZN B 501 O1 GOL B 502 1555 1555 2.52 LINK ZN ZN B 501 O2 GOL B 502 1555 1555 1.91 CISPEP 1 GLY A 144 PRO A 145 0 7.51 CISPEP 2 GLY B 144 PRO B 145 0 8.26 CRYST1 61.777 84.336 154.166 90.00 90.00 90.00 P 21 21 21 8 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 0.016187 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006487 0.00000