HEADER TRANSFERASE 13-JUL-15 5CIU TITLE STRUCTURAL BASIS OF THE RECOGNITION OF H3K36ME3 BY DNMT3B PWWP DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DNMT3B,DNA METHYLTRANSFERASE HSAIIIB,M.HSAIIIB; COMPND 5 EC: 2.1.1.37; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE H3.2; COMPND 9 CHAIN: C, D; COMPND 10 SYNONYM: HISTONE H3/M,HISTONE H3/O; 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: DNMT3B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS PROTEIN-PEPTIDE COMPLEX, DNMT3B, PWWP DOMAIN, HISTONE BINDING, KEYWDS 2 H3K36ME3, METHYLTRANSFERASE 3 BETA, S-ADENOSYL-L-METHIONINE, KEYWDS 3 TRANSFERASE, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR G.RONDELET,T.DAL MASO,L.WILLEMS,J.WOUTERS REVDAT 4 10-JAN-24 5CIU 1 REMARK REVDAT 3 12-JUN-19 5CIU 1 AUTHOR REMARK ATOM REVDAT 2 04-MAY-16 5CIU 1 JRNL REVDAT 1 30-MAR-16 5CIU 0 JRNL AUTH G.RONDELET,T.DAL MASO,L.WILLEMS,J.WOUTERS JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF HISTONE H3K36ME3 JRNL TITL 2 NUCLEOSOME BY HUMAN DE NOVO DNA METHYLTRANSFERASES 3A AND JRNL TITL 3 3B. JRNL REF J.STRUCT.BIOL. V. 194 357 2016 JRNL REFN ESSN 1095-8657 JRNL PMID 26993463 JRNL DOI 10.1016/J.JSB.2016.03.013 REMARK 2 REMARK 2 RESOLUTION. 2.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 24436 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1905 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 36.7234 - 5.3935 0.97 1694 148 0.2347 0.2472 REMARK 3 2 5.3935 - 4.2831 1.00 1653 141 0.1836 0.2014 REMARK 3 3 4.2831 - 3.7423 1.00 1632 133 0.1904 0.1851 REMARK 3 4 3.7423 - 3.4004 1.00 1633 136 0.1978 0.2501 REMARK 3 5 3.4004 - 3.1568 1.00 1616 132 0.2253 0.2806 REMARK 3 6 3.1568 - 2.9708 1.00 1606 132 0.2465 0.3166 REMARK 3 7 2.9708 - 2.8220 1.00 1571 135 0.2481 0.3184 REMARK 3 8 2.8220 - 2.6992 1.00 1612 140 0.2564 0.3434 REMARK 3 9 2.6992 - 2.5954 1.00 1596 135 0.2609 0.3185 REMARK 3 10 2.5954 - 2.5058 1.00 1584 134 0.2736 0.3266 REMARK 3 11 2.5058 - 2.4275 1.00 1582 136 0.2885 0.3455 REMARK 3 12 2.4275 - 2.3581 1.00 1580 134 0.2788 0.3145 REMARK 3 13 2.3581 - 2.2960 1.00 1568 133 0.2992 0.3533 REMARK 3 14 2.2960 - 2.2400 1.00 1604 136 0.3168 0.3815 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) : 27.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.45 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 2162 REMARK 3 ANGLE : 1.204 2898 REMARK 3 CHIRALITY : 0.087 282 REMARK 3 PLANARITY : 0.005 354 REMARK 3 DIHEDRAL : 13.937 774 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 5CIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-14 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : CRYOGENICALLY COOLED CHANNEL-CUT REMARK 200 SI[111] REMARK 200 OPTICS : X-RAY FLUORESCCENCE DETECTOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24436 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.63300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.950 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.2 REMARK 200 STARTING MODEL: 3QKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M SODIUM CITRATE TRIBASIC, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 105.46667 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 52.73333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.73333 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 105.46667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 HOH A 416 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 GLU A 206 REMARK 465 ALA A 207 REMARK 465 ASP A 208 REMARK 465 SER A 209 REMARK 465 GLY A 210 REMARK 465 ASP A 211 REMARK 465 GLY A 212 REMARK 465 ASP A 213 REMARK 465 SER A 214 REMARK 465 SER A 215 REMARK 465 PRO A 318 REMARK 465 SER A 319 REMARK 465 SER A 320 REMARK 465 PRO A 321 REMARK 465 GLY A 322 REMARK 465 ASP A 323 REMARK 465 SER A 324 REMARK 465 LEU A 325 REMARK 465 GLU A 326 REMARK 465 ASN A 352 REMARK 465 THR A 353 REMARK 465 GLN A 354 REMARK 465 PRO A 355 REMARK 465 GLU B 206 REMARK 465 ALA B 207 REMARK 465 ASP B 208 REMARK 465 SER B 209 REMARK 465 GLY B 210 REMARK 465 ASP B 211 REMARK 465 GLY B 212 REMARK 465 ASP B 213 REMARK 465 SER B 214 REMARK 465 SER B 215 REMARK 465 ALA B 290 REMARK 465 THR B 291 REMARK 465 THR B 316 REMARK 465 PHE B 317 REMARK 465 PRO B 318 REMARK 465 SER B 319 REMARK 465 SER B 320 REMARK 465 PRO B 321 REMARK 465 GLY B 322 REMARK 465 ASP B 323 REMARK 465 SER B 324 REMARK 465 LEU B 325 REMARK 465 GLU B 326 REMARK 465 ASP B 327 REMARK 465 GLN B 328 REMARK 465 ASN B 352 REMARK 465 THR B 353 REMARK 465 GLN B 354 REMARK 465 PRO B 355 REMARK 465 SER C 28 REMARK 465 ALA C 29 REMARK 465 PRO C 30 REMARK 465 ALA C 31 REMARK 465 HIS C 39 REMARK 465 ARG C 40 REMARK 465 TYR C 41 REMARK 465 ARG C 42 REMARK 465 SER D 28 REMARK 465 ALA D 29 REMARK 465 PRO D 30 REMARK 465 ALA D 31 REMARK 465 HIS D 39 REMARK 465 ARG D 40 REMARK 465 TYR D 41 REMARK 465 ARG D 42 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 234 CG CD CE NZ REMARK 480 LYS B 234 CB CG CD CE NZ REMARK 480 LYS B 330 CB CG CD CE NZ REMARK 480 GLU B 334 CB CG CD OE1 OE2 REMARK 480 LYS B 341 CB CG CD CE NZ 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 NZ LYS A 232 O PHE A 236 2.04 REMARK 500 O PRO A 342 O HOH A 401 2.13 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 PHE A 223 138.10 79.94 REMARK 500 LYS A 251 -98.58 -117.30 REMARK 500 THR A 316 -63.14 -109.18 REMARK 500 TYR B 217 19.15 81.94 REMARK 500 LYS B 251 -95.83 -108.55 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 496 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A 497 DISTANCE = 7.83 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 401 DBREF 5CIU A 206 355 UNP Q9UBC3 DNM3B_HUMAN 206 355 DBREF 5CIU B 206 355 UNP Q9UBC3 DNM3B_HUMAN 206 355 DBREF 5CIU C 28 42 PDB 5CIU 5CIU 28 42 DBREF 5CIU D 28 42 PDB 5CIU 5CIU 28 42 SEQRES 1 A 150 GLU ALA ASP SER GLY ASP GLY ASP SER SER GLU TYR GLN SEQRES 2 A 150 ASP GLY LYS GLU PHE GLY ILE GLY ASP LEU VAL TRP GLY SEQRES 3 A 150 LYS ILE LYS GLY PHE SER TRP TRP PRO ALA MET VAL VAL SEQRES 4 A 150 SER TRP LYS ALA THR SER LYS ARG GLN ALA MET SER GLY SEQRES 5 A 150 MET ARG TRP VAL GLN TRP PHE GLY ASP GLY LYS PHE SER SEQRES 6 A 150 GLU VAL SER ALA ASP LYS LEU VAL ALA LEU GLY LEU PHE SEQRES 7 A 150 SER GLN HIS PHE ASN LEU ALA THR PHE ASN LYS LEU VAL SEQRES 8 A 150 SER TYR ARG LYS ALA MET TYR HIS ALA LEU GLU LYS ALA SEQRES 9 A 150 ARG VAL ARG ALA GLY LYS THR PHE PRO SER SER PRO GLY SEQRES 10 A 150 ASP SER LEU GLU ASP GLN LEU LYS PRO MET LEU GLU TRP SEQRES 11 A 150 ALA HIS GLY GLY PHE LYS PRO THR GLY ILE GLU GLY LEU SEQRES 12 A 150 LYS PRO ASN ASN THR GLN PRO SEQRES 1 B 150 GLU ALA ASP SER GLY ASP GLY ASP SER SER GLU TYR GLN SEQRES 2 B 150 ASP GLY LYS GLU PHE GLY ILE GLY ASP LEU VAL TRP GLY SEQRES 3 B 150 LYS ILE LYS GLY PHE SER TRP TRP PRO ALA MET VAL VAL SEQRES 4 B 150 SER TRP LYS ALA THR SER LYS ARG GLN ALA MET SER GLY SEQRES 5 B 150 MET ARG TRP VAL GLN TRP PHE GLY ASP GLY LYS PHE SER SEQRES 6 B 150 GLU VAL SER ALA ASP LYS LEU VAL ALA LEU GLY LEU PHE SEQRES 7 B 150 SER GLN HIS PHE ASN LEU ALA THR PHE ASN LYS LEU VAL SEQRES 8 B 150 SER TYR ARG LYS ALA MET TYR HIS ALA LEU GLU LYS ALA SEQRES 9 B 150 ARG VAL ARG ALA GLY LYS THR PHE PRO SER SER PRO GLY SEQRES 10 B 150 ASP SER LEU GLU ASP GLN LEU LYS PRO MET LEU GLU TRP SEQRES 11 B 150 ALA HIS GLY GLY PHE LYS PRO THR GLY ILE GLU GLY LEU SEQRES 12 B 150 LYS PRO ASN ASN THR GLN PRO SEQRES 1 C 15 SER ALA PRO ALA THR GLY GLY VAL M3L LYS PRO HIS ARG SEQRES 2 C 15 TYR ARG SEQRES 1 D 15 SER ALA PRO ALA THR GLY GLY VAL M3L LYS PRO HIS ARG SEQRES 2 D 15 TYR ARG MODRES 5CIU M3L C 36 LYS MODIFIED RESIDUE MODRES 5CIU M3L D 36 LYS MODIFIED RESIDUE HET M3L C 36 12 HET M3L D 36 12 HET GOL B 401 6 HETNAM M3L N-TRIMETHYLLYSINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 M3L 2(C9 H21 N2 O2 1+) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *163(H2 O) HELIX 1 AA1 SER A 245 THR A 249 5 5 HELIX 2 AA2 ASN A 288 LEU A 295 1 8 HELIX 3 AA3 LEU A 295 GLY A 314 1 20 HELIX 4 AA4 GLN A 328 GLY A 338 1 11 HELIX 5 AA5 GLY A 344 LYS A 349 5 6 HELIX 6 AA6 SER B 245 THR B 249 5 5 HELIX 7 AA7 ASP B 275 LEU B 277 5 3 HELIX 8 AA8 LEU B 282 PHE B 287 1 6 HELIX 9 AA9 LEU B 295 GLY B 314 1 20 HELIX 10 AB1 LYS B 330 GLY B 338 1 9 HELIX 11 AB2 GLY B 344 LEU B 348 5 5 SHEET 1 AA1 5 PHE A 269 SER A 273 0 SHEET 2 AA1 5 MET A 258 TRP A 263 -1 N ARG A 259 O VAL A 272 SHEET 3 AA1 5 TRP A 239 VAL A 244 -1 N MET A 242 O GLN A 262 SHEET 4 AA1 5 LEU A 228 GLY A 231 -1 N VAL A 229 O ALA A 241 SHEET 5 AA1 5 LEU A 277 ALA A 279 -1 O VAL A 278 N TRP A 230 SHEET 1 AA2 5 PHE B 269 SER B 273 0 SHEET 2 AA2 5 MET B 258 TRP B 263 -1 N ARG B 259 O VAL B 272 SHEET 3 AA2 5 TRP B 239 VAL B 244 -1 N MET B 242 O GLN B 262 SHEET 4 AA2 5 LEU B 228 GLY B 231 -1 N VAL B 229 O ALA B 241 SHEET 5 AA2 5 VAL B 278 ALA B 279 -1 O VAL B 278 N TRP B 230 LINK C VAL C 35 N M3L C 36 1555 1555 1.33 LINK C M3L C 36 N LYS C 37 1555 1555 1.33 LINK C VAL D 35 N M3L D 36 1555 1555 1.34 LINK C M3L D 36 N LYS D 37 1555 1555 1.33 CISPEP 1 LYS A 341 PRO A 342 0 9.11 CISPEP 2 ASP B 219 GLY B 220 0 -3.61 CISPEP 3 LYS B 341 PRO B 342 0 5.53 SITE 1 AC1 2 ARG B 252 VAL C 35 CRYST1 73.437 73.437 158.200 90.00 90.00 120.00 P 32 2 1 12 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 0.013617 0.007862 0.000000 0.00000 SCALE2 0.000000 0.015724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006321 0.00000