HEADER LUMINESCENT PROTEIN 04-MAY-17 5VP3 TITLE LIGHT-SENSITIVE PHOTOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MNEMIOPSIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOTOPROTEIN 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MNEMIOPSIS LEIDYI; SOURCE 3 ORGANISM_COMMON: SEA WALNUT; SOURCE 4 ORGANISM_TAXID: 27923; SOURCE 5 GENE: PP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BIOLUMINESCENCE, CTENOPHORE, CA(2+)-REGULATED PHOTOPROTEIN, EF-HAND, KEYWDS 2 MNEMIOPSIS LEIDYI, MNEMIOPSIN 1, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.GORMAN,M.W.PARKER REVDAT 3 04-OCT-23 5VP3 1 LINK REVDAT 2 16-JAN-19 5VP3 1 COMPND SOURCE JRNL REMARK REVDAT 2 2 1 DBREF SEQRES LINK SITE REVDAT 2 3 1 ATOM REVDAT 1 09-MAY-18 5VP3 0 JRNL AUTH M.MOLAKARIMI,M.A.GORMAN,A.MOHSENI,Z.PASHANDI,M.TAGHDIR, JRNL AUTH 2 H.NADERI-MANESH,R.H.SAJEDI,M.W.PARKER JRNL TITL REACTION MECHANISM OF THE BIOLUMINESCENT PROTEIN MNEMIOPSIN1 JRNL TITL 2 REVEALED BY X-RAY CRYSTALLOGRAPHY AND QM/MM SIMULATIONS. JRNL REF J. BIOL. CHEM. V. 294 20 2019 JRNL REFN ESSN 1083-351X JRNL PMID 30420427 JRNL DOI 10.1074/JBC.RA118.006053 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.670 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 13301 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 1191 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 34.1811 - 4.4718 1.00 2746 147 0.1448 0.1636 REMARK 3 2 4.4718 - 3.5506 1.00 2780 126 0.1326 0.1607 REMARK 3 3 3.5506 - 3.1021 1.00 2793 111 0.1665 0.2594 REMARK 3 4 3.1021 - 2.8186 1.00 2729 142 0.1783 0.2104 REMARK 3 5 2.8186 - 2.6167 1.00 2755 148 0.1868 0.2037 REMARK 3 6 2.6167 - 2.4624 1.00 2801 124 0.1739 0.2494 REMARK 3 7 2.4624 - 2.3391 1.00 2741 103 0.1731 0.2401 REMARK 3 8 2.3391 - 2.2373 1.00 2780 149 0.1795 0.2722 REMARK 3 9 2.2373 - 2.1512 0.97 2657 141 0.2060 0.2414 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.21 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 : 0.012 1702 REMARK 3 ANGLE : 1.185 2300 REMARK 3 CHIRALITY : 0.055 234 REMARK 3 PLANARITY : 0.007 307 REMARK 3 DIHEDRAL : 14.227 1030 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 5VP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13301 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 16.90 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 14.30 REMARK 200 R MERGE FOR SHELL (I) : 0.63700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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: 5BPJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM TIOCYANATE, 20% (W/V) REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 54.28600 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 27.14300 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 40.71450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.57150 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.85750 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 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 PRO A 196 REMARK 465 GLN A 197 REMARK 465 TRP A 198 REMARK 465 ASP A 199 REMARK 465 GLY A 200 REMARK 465 VAL A 201 REMARK 465 TYR A 202 REMARK 465 ALA A 203 REMARK 465 TYR A 204 REMARK 465 LYS A 205 REMARK 465 TYR A 206 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 HH22 ARG A 115 O HOH A 401 1.17 REMARK 500 HE ARG A 187 O HOH A 404 1.41 REMARK 500 HH TYR A 37 O HOH A 405 1.56 REMARK 500 NH2 ARG A 115 O HOH A 401 2.02 REMARK 500 O HOH A 452 O HOH A 507 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 116 CD GLU A 116 OE2 -0.068 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES 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 MET A 191 -58.93 -161.09 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 CD A 301 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 44 OD1 REMARK 620 2 ASP A 46 OD1 75.0 REMARK 620 3 ASP A 48 OD1 84.3 85.8 REMARK 620 4 LYS A 50 O 83.3 153.6 77.0 REMARK 620 5 GLU A 55 OE2 95.7 73.6 158.7 124.3 REMARK 620 6 HOH A 424 O 170.5 101.5 86.7 97.5 91.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 304 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 82 NE2 REMARK 620 2 GLU A 192 OE1 35.4 REMARK 620 3 GLU A 192 OE2 32.8 3.8 REMARK 620 4 HOH A 495 O 32.7 3.1 4.0 REMARK 620 5 HOH A 496 O 34.0 5.7 3.0 6.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 302 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 136 OD1 REMARK 620 2 ASP A 140 OD1 82.1 REMARK 620 3 THR A 142 O 82.7 78.2 REMARK 620 4 GLU A 147 OE1 88.8 154.2 124.7 REMARK 620 5 GLU A 147 OE2 113.6 150.7 79.6 54.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 303 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 170 OD1 REMARK 620 2 THR A 174 OG1 87.2 REMARK 620 3 LYS A 176 O 87.0 70.4 REMARK 620 4 GLU A 178 OE1 171.4 84.4 88.4 REMARK 620 5 GLU A 181 OE1 107.6 149.1 83.1 79.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 305 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 184 ND1 REMARK 620 2 HOH A 463 O 99.5 REMARK 620 3 HOH A 498 O 88.4 100.1 REMARK 620 4 HOH A 515 O 161.8 66.5 83.1 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 CD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 306 DBREF 5VP3 A 1 206 UNP E0WVU4 E0WVU4_MNELE 1 206 SEQRES 1 A 206 MET PRO LEU ASP GLU THR ASN ASN GLU SER TYR ARG TYR SEQRES 2 A 206 LEU ARG SER VAL GLY ASN THR TRP LYS PHE ASN VAL GLU SEQRES 3 A 206 ASP VAL HIS PRO LYS MET LEU GLU ARG LEU TYR LYS ARG SEQRES 4 A 206 PHE ASP THR PHE ASP LEU ASP THR ASP GLY LYS MET THR SEQRES 5 A 206 MET ASP GLU ILE MET TYR TRP PRO ASP ARG MET ARG GLN SEQRES 6 A 206 LEU VAL ASN ALA THR ASP GLU GLN VAL GLU LYS MET ARG SEQRES 7 A 206 ALA ALA VAL HIS THR PHE PHE PHE HIS LYS GLY VAL ASP SEQRES 8 A 206 PRO VAL ASN GLY LEU LYS ARG GLU ASP TRP VAL GLU ALA SEQRES 9 A 206 ASN ARG VAL PHE ALA GLU ALA GLU ARG GLU ARG GLU ARG SEQRES 10 A 206 ARG GLY GLU PRO SER LEU ILE ALA LEU LEU SER ASN ALA SEQRES 11 A 206 TYR TYR ASP VAL LEU ASP ASP ASP GLY ASP GLY THR VAL SEQRES 12 A 206 ASP VAL GLU GLU LEU LYS THR MET MET LYS ALA PHE ASP SEQRES 13 A 206 VAL PRO GLN GLU ALA ALA TYR THR PHE PHE GLN LYS ALA SEQRES 14 A 206 ASP THR ASP LYS THR GLY LYS LEU GLU ARG PRO GLU LEU SEQRES 15 A 206 VAL HIS LEU PHE ARG LYS PHE TRP MET GLU PRO TYR ASP SEQRES 16 A 206 PRO GLN TRP ASP GLY VAL TYR ALA TYR LYS TYR HET CD A 301 1 HET CD A 302 1 HET CD A 303 1 HET CD A 304 1 HET NI A 305 1 HET SCN A 306 3 HETNAM CD CADMIUM ION HETNAM NI NICKEL (II) ION HETNAM SCN THIOCYANATE ION FORMUL 2 CD 4(CD 2+) FORMUL 6 NI NI 2+ FORMUL 7 SCN C N S 1- FORMUL 8 HOH *118(H2 O) HELIX 1 AA1 ASN A 8 VAL A 17 1 10 HELIX 2 AA2 ASN A 24 VAL A 28 5 5 HELIX 3 AA3 HIS A 29 ASP A 44 1 16 HELIX 4 AA4 THR A 52 VAL A 67 1 16 HELIX 5 AA5 THR A 70 LYS A 88 1 19 HELIX 6 AA6 ASP A 100 ARG A 118 1 19 HELIX 7 AA7 SER A 122 ASP A 136 1 15 HELIX 8 AA8 ASP A 144 PHE A 155 1 12 HELIX 9 AA9 GLU A 160 ASP A 170 1 11 HELIX 10 AB1 GLU A 178 MET A 191 1 14 SHEET 1 AA1 2 LYS A 50 MET A 51 0 SHEET 2 AA1 2 LEU A 96 LYS A 97 -1 O LEU A 96 N MET A 51 LINK OD1 ASP A 44 CD CD A 301 1555 1555 2.17 LINK OD1 ASP A 46 CD CD A 301 1555 1555 2.29 LINK OD1 ASP A 48 CD CD A 301 1555 1555 2.40 LINK O LYS A 50 CD CD A 301 1555 1555 2.30 LINK OE2 GLU A 55 CD CD A 301 1555 1555 2.37 LINK NE2 HIS A 82 CD CD A 304 1555 6654 2.39 LINK OD1 ASP A 136 CD CD A 302 1555 1555 2.25 LINK OD1 ASP A 140 CD CD A 302 1555 1555 2.26 LINK O THR A 142 CD CD A 302 1555 1555 2.38 LINK OE1 GLU A 147 CD CD A 302 1555 1555 2.45 LINK OE2 GLU A 147 CD CD A 302 1555 1555 2.21 LINK OD1 ASP A 170 CD CD A 303 1555 1555 2.23 LINK OG1 THR A 174 CD CD A 303 1555 1555 2.53 LINK O LYS A 176 CD CD A 303 1555 1555 2.38 LINK OE1 GLU A 178 CD CD A 303 1555 1555 2.16 LINK OE1 GLU A 181 CD CD A 303 1555 1555 2.35 LINK ND1 HIS A 184 NI NI A 305 1555 1555 2.04 LINK OE1 GLU A 192 CD CD A 304 1555 1555 2.62 LINK OE2 GLU A 192 CD CD A 304 1555 1555 2.68 LINK CD CD A 301 O HOH A 424 1555 1555 2.46 LINK CD CD A 304 O HOH A 495 1555 1555 2.66 LINK CD CD A 304 O HOH A 496 1555 1555 2.62 LINK NI NI A 305 O HOH A 463 1555 5565 2.64 LINK NI NI A 305 O HOH A 498 1555 1555 2.77 LINK NI NI A 305 O HOH A 515 1555 5565 2.76 SITE 1 AC1 6 ASP A 44 ASP A 46 ASP A 48 LYS A 50 SITE 2 AC1 6 GLU A 55 HOH A 424 SITE 1 AC2 6 ASP A 136 ASP A 138 ASP A 140 THR A 142 SITE 2 AC2 6 GLU A 147 HOH A 402 SITE 1 AC3 6 ASP A 170 ASP A 172 THR A 174 LYS A 176 SITE 2 AC3 6 GLU A 178 GLU A 181 SITE 1 AC4 5 HIS A 82 GLU A 192 HOH A 495 HOH A 496 SITE 2 AC4 5 HOH A 508 SITE 1 AC5 4 HIS A 184 HOH A 463 HOH A 498 HOH A 515 SITE 1 AC6 4 GLN A 73 ASP A 133 ASP A 136 HOH A 467 CRYST1 72.614 72.614 81.429 90.00 90.00 120.00 P 65 6 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 0.013771 0.007951 0.000000 0.00000 SCALE2 0.000000 0.015902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012281 0.00000