HEADER OXIDOREDUCTASE/TRANSCRIPTION/RNA 16-DEC-14 4XBF TITLE STRUCTURE OF LSD1:COREST IN COMPLEX WITH SSRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 171-836; COMPND 5 SYNONYM: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE COMPND 6 OXIDASE DOMAIN-CONTAINING PROTEIN 2; COMPND 7 EC: 1.-.-.-; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: RECOMBINANT PLASMID (RESIDUES 171-852); COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: REST COREPRESSOR 1; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: UNP RESIDUES 308-440; COMPND 14 SYNONYM: PROTEIN COREST; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: AMINO ACIDS RESIDUES 286-482, GIFT FROM DR. PHILLIP COMPND 17 COLE.; COMPND 18 MOL_ID: 3; COMPND 19 MOLECULE: RNA (5'-R(*UP*UP*AP*GP*G)-3'); COMPND 20 CHAIN: D; COMPND 21 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: KDM1A, AOF2, KDM1, KIAA0601, LSD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: RCOR1, KIAA0071, RCOR; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE); SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_TAXID: 9606 KEYWDS LSD1, LYSINE SPECIFIC DEMETHYLASE, DEMETHYLASE, DEMETHYLATION, RNA, KEYWDS 2 COREST, REST CO-REPRESSOR 1, AMINE OXIDASE, COILED-COIL, SWIRM, KEYWDS 3 CHROMATIN REMODELLING ENZYME, EPIGENETICS, HISTONE MODIFYING ENZYME, KEYWDS 4 NON-CODING RNA, NCRNA, KDM1A, OXIDOREDUCTASE-TRANSCRIPTION-RNA KEYWDS 5 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.LUKA,L.V.LOUKACHEVITCH,W.J.MARTIN,C.WAGNER,N.J.REITER REVDAT 3 27-SEP-23 4XBF 1 REMARK REVDAT 2 03-MAY-17 4XBF 1 JRNL REMARK REVDAT 1 27-APR-16 4XBF 0 JRNL AUTH A.HIRSCHI,W.J.MARTIN,Z.LUKA,L.V.LOUKACHEVITCH,N.J.REITER JRNL TITL G-QUADRUPLEX RNA BINDING AND RECOGNITION BY THE JRNL TITL 2 LYSINE-SPECIFIC HISTONE DEMETHYLASE-1 ENZYME. JRNL REF RNA V. 22 1250 2016 JRNL REFN ESSN 1469-9001 JRNL PMID 27277658 JRNL DOI 10.1261/RNA.057265.116 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1839) 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 62268 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.210 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 49.0253 - 6.7505 0.99 4504 150 0.1755 0.1829 REMARK 3 2 6.7505 - 5.3602 1.00 4398 147 0.1927 0.2363 REMARK 3 3 5.3602 - 4.6832 1.00 4328 143 0.1653 0.1737 REMARK 3 4 4.6832 - 4.2553 1.00 4359 144 0.1577 0.1633 REMARK 3 5 4.2553 - 3.9505 1.00 4330 144 0.1748 0.2424 REMARK 3 6 3.9505 - 3.7176 1.00 4278 142 0.1952 0.2522 REMARK 3 7 3.7176 - 3.5315 1.00 4318 143 0.2143 0.2456 REMARK 3 8 3.5315 - 3.3778 1.00 4284 142 0.2223 0.2201 REMARK 3 9 3.3778 - 3.2478 1.00 4291 143 0.2396 0.2506 REMARK 3 10 3.2478 - 3.1358 1.00 4294 142 0.2523 0.2732 REMARK 3 11 3.1358 - 3.0377 1.00 4279 142 0.2630 0.3069 REMARK 3 12 3.0377 - 2.9509 1.00 4255 141 0.2750 0.2859 REMARK 3 13 2.9509 - 2.8732 0.99 4277 141 0.2749 0.3261 REMARK 3 14 2.8732 - 2.8030 0.96 4073 136 0.2894 0.3255 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.80 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 : 0.003 6600 REMARK 3 ANGLE : 0.743 8974 REMARK 3 CHIRALITY : 0.027 1004 REMARK 3 PLANARITY : 0.004 1138 REMARK 3 DIHEDRAL : 14.966 2472 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 4XBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6-6.4 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND (C111) REMARK 200 OPTICS : 12.7 KEV ENERGY RANGE, FOCUSED REMARK 200 BEAM SIZE: 50UM X 50UM REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 VERSION V706 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62270 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.803 REMARK 200 RESOLUTION RANGE LOW (A) : 49.018 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 14.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 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: NULL REMARK 200 STARTING MODEL: 2IW5 REMARK 200 REMARK 200 REMARK: ORTHORHOMBIC I222 SPACE GROUP REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE LSD1-COREST COMPLEX 10-12 MG/ML REMARK 280 CONCENTRATION (IN 25 MM HEPES-NA, PH 7.4, 100 MM NACL, 5 MM DTT, REMARK 280 1 MM PMSF) WAS MIXED (1:1) WITH THE RESERVOIR SOLUTION [0.60 M REMARK 280 LI2SO4, 0.63 M (NH4)2SO4, 0.25 M NACL, 100 MM NA-CITRATE, PH 5.6, REMARK 280 10 MM DTT], VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 60.53650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 89.20550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 117.33800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.53650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 89.20550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 117.33800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.53650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.20550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 117.33800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.53650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 89.20550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 117.33800 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 42310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 145990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -539.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 BIOMT1 2 -1.000000 0.000000 0.000000 363.21900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 178.41100 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 363.21900 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 178.41100 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 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 G D 5 C5' C4' O4' C3' O3' C2' O2' REMARK 470 G D 5 C1' N9 C8 N7 C5 C6 O6 REMARK 470 G D 5 N1 C2 N2 N3 C4 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 526 O2 GOL A 907 1.59 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 ILE A 270 -73.18 -96.96 REMARK 500 MET A 332 -35.52 -143.31 REMARK 500 ASN A 350 49.37 -73.80 REMARK 500 LEU A 401 114.16 -165.58 REMARK 500 ASN A 514 69.00 -117.71 REMARK 500 LYS A 699 72.70 -65.84 REMARK 500 LYS A 744 -73.22 -72.00 REMARK 500 ALA A 757 -54.32 -142.36 REMARK 500 SER A 760 -61.62 -99.22 REMARK 500 ARG A 795 -25.28 -143.24 REMARK 500 ASN B 327 -162.23 -167.39 REMARK 500 CYS B 379 152.69 -47.15 REMARK 500 TYR B 424 45.06 -102.37 REMARK 500 ARG B 426 -23.31 -143.99 REMARK 500 ALA B 439 31.98 -83.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 907 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KUM RELATED DB: PDB DBREF 4XBF A 171 836 UNP O60341 KDM1A_HUMAN 171 836 DBREF 4XBF B 308 440 UNP Q9UKL0 RCOR1_HUMAN 308 440 DBREF 4XBF D 1 5 PDB 4XBF 4XBF 1 5 SEQRES 1 A 666 PRO SER GLY VAL GLU GLY ALA ALA PHE GLN SER ARG LEU SEQRES 2 A 666 PRO HIS ASP ARG MET THR SER GLN GLU ALA ALA CYS PHE SEQRES 3 A 666 PRO ASP ILE ILE SER GLY PRO GLN GLN THR GLN LYS VAL SEQRES 4 A 666 PHE LEU PHE ILE ARG ASN ARG THR LEU GLN LEU TRP LEU SEQRES 5 A 666 ASP ASN PRO LYS ILE GLN LEU THR PHE GLU ALA THR LEU SEQRES 6 A 666 GLN GLN LEU GLU ALA PRO TYR ASN SER ASP THR VAL LEU SEQRES 7 A 666 VAL HIS ARG VAL HIS SER TYR LEU GLU ARG HIS GLY LEU SEQRES 8 A 666 ILE ASN PHE GLY ILE TYR LYS ARG ILE LYS PRO LEU PRO SEQRES 9 A 666 THR LYS LYS THR GLY LYS VAL ILE ILE ILE GLY SER GLY SEQRES 10 A 666 VAL SER GLY LEU ALA ALA ALA ARG GLN LEU GLN SER PHE SEQRES 11 A 666 GLY MET ASP VAL THR LEU LEU GLU ALA ARG ASP ARG VAL SEQRES 12 A 666 GLY GLY ARG VAL ALA THR PHE ARG LYS GLY ASN TYR VAL SEQRES 13 A 666 ALA ASP LEU GLY ALA MET VAL VAL THR GLY LEU GLY GLY SEQRES 14 A 666 ASN PRO MET ALA VAL VAL SER LYS GLN VAL ASN MET GLU SEQRES 15 A 666 LEU ALA LYS ILE LYS GLN LYS CYS PRO LEU TYR GLU ALA SEQRES 16 A 666 ASN GLY GLN ALA VAL PRO LYS GLU LYS ASP GLU MET VAL SEQRES 17 A 666 GLU GLN GLU PHE ASN ARG LEU LEU GLU ALA THR SER TYR SEQRES 18 A 666 LEU SER HIS GLN LEU ASP PHE ASN VAL LEU ASN ASN LYS SEQRES 19 A 666 PRO VAL SER LEU GLY GLN ALA LEU GLU VAL VAL ILE GLN SEQRES 20 A 666 LEU GLN GLU LYS HIS VAL LYS ASP GLU GLN ILE GLU HIS SEQRES 21 A 666 TRP LYS LYS ILE VAL LYS THR GLN GLU GLU LEU LYS GLU SEQRES 22 A 666 LEU LEU ASN LYS MET VAL ASN LEU LYS GLU LYS ILE LYS SEQRES 23 A 666 GLU LEU HIS GLN GLN TYR LYS GLU ALA SER GLU VAL LYS SEQRES 24 A 666 PRO PRO ARG ASP ILE THR ALA GLU PHE LEU VAL LYS SER SEQRES 25 A 666 LYS HIS ARG ASP LEU THR ALA LEU CYS LYS GLU TYR ASP SEQRES 26 A 666 GLU LEU ALA GLU THR GLN GLY LYS LEU GLU GLU LYS LEU SEQRES 27 A 666 GLN GLU LEU GLU ALA ASN PRO PRO SER ASP VAL TYR LEU SEQRES 28 A 666 SER SER ARG ASP ARG GLN ILE LEU ASP TRP HIS PHE ALA SEQRES 29 A 666 ASN LEU GLU PHE ALA ASN ALA THR PRO LEU SER THR LEU SEQRES 30 A 666 SER LEU LYS HIS TRP ASP GLN ASP ASP ASP PHE GLU PHE SEQRES 31 A 666 THR GLY SER HIS LEU THR VAL ARG ASN GLY TYR SER CYS SEQRES 32 A 666 VAL PRO VAL ALA LEU ALA GLU GLY LEU ASP ILE LYS LEU SEQRES 33 A 666 ASN THR ALA VAL ARG GLN VAL ARG TYR THR ALA SER GLY SEQRES 34 A 666 CYS GLU VAL ILE ALA VAL ASN THR ARG SER THR SER GLN SEQRES 35 A 666 THR PHE ILE TYR LYS CYS ASP ALA VAL LEU CYS THR LEU SEQRES 36 A 666 PRO LEU GLY VAL LEU LYS GLN GLN PRO PRO ALA VAL GLN SEQRES 37 A 666 PHE VAL PRO PRO LEU PRO GLU TRP LYS THR SER ALA VAL SEQRES 38 A 666 GLN ARG MET GLY PHE GLY ASN LEU ASN LYS VAL VAL LEU SEQRES 39 A 666 CYS PHE ASP ARG VAL PHE TRP ASP PRO SER VAL ASN LEU SEQRES 40 A 666 PHE GLY HIS VAL GLY SER THR THR ALA SER ARG GLY GLU SEQRES 41 A 666 LEU PHE LEU PHE TRP ASN LEU TYR LYS ALA PRO ILE LEU SEQRES 42 A 666 LEU ALA LEU VAL ALA GLY GLU ALA ALA GLY ILE MET GLU SEQRES 43 A 666 ASN ILE SER ASP ASP VAL ILE VAL GLY ARG CYS LEU ALA SEQRES 44 A 666 ILE LEU LYS GLY ILE PHE GLY SER SER ALA VAL PRO GLN SEQRES 45 A 666 PRO LYS GLU THR VAL VAL SER ARG TRP ARG ALA ASP PRO SEQRES 46 A 666 TRP ALA ARG GLY SER TYR SER TYR VAL ALA ALA GLY SER SEQRES 47 A 666 SER GLY ASN ASP TYR ASP LEU MET ALA GLN PRO ILE THR SEQRES 48 A 666 PRO GLY PRO SER ILE PRO GLY ALA PRO GLN PRO ILE PRO SEQRES 49 A 666 ARG LEU PHE PHE ALA GLY GLU HIS THR ILE ARG ASN TYR SEQRES 50 A 666 PRO ALA THR VAL HIS GLY ALA LEU LEU SER GLY LEU ARG SEQRES 51 A 666 GLU ALA GLY ARG ILE ALA ASP GLN PHE LEU GLY ALA MET SEQRES 52 A 666 TYR THR LEU SEQRES 1 B 133 ARG LYS PRO PRO LYS GLY MET PHE LEU SER GLN GLU ASP SEQRES 2 B 133 VAL GLU ALA VAL SER ALA ASN ALA THR ALA ALA THR THR SEQRES 3 B 133 VAL LEU ARG GLN LEU ASP MET GLU LEU VAL SER VAL LYS SEQRES 4 B 133 ARG GLN ILE GLN ASN ILE LYS GLN THR ASN SER ALA LEU SEQRES 5 B 133 LYS GLU LYS LEU ASP GLY GLY ILE GLU PRO TYR ARG LEU SEQRES 6 B 133 PRO GLU VAL ILE GLN LYS CYS ASN ALA ARG TRP THR THR SEQRES 7 B 133 GLU GLU GLN LEU LEU ALA VAL GLN ALA ILE ARG LYS TYR SEQRES 8 B 133 GLY ARG ASP PHE GLN ALA ILE SER ASP VAL ILE GLY ASN SEQRES 9 B 133 LYS SER VAL VAL GLN VAL LYS ASN PHE PHE VAL ASN TYR SEQRES 10 B 133 ARG ARG ARG PHE ASN ILE ASP GLU VAL LEU GLN GLU TRP SEQRES 11 B 133 GLU ALA GLU SEQRES 1 D 5 U U A G G HET FAD A 901 84 HET SO4 A 902 5 HET SO4 A 903 5 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 A 906 5 HET GOL A 907 14 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 SO4 5(O4 S 2-) FORMUL 10 GOL C3 H8 O3 FORMUL 11 HOH *23(H2 O) HELIX 1 AA1 GLY A 173 SER A 181 1 9 HELIX 2 AA2 THR A 189 PHE A 196 1 8 HELIX 3 AA3 PHE A 196 SER A 201 1 6 HELIX 4 AA4 PRO A 203 ASN A 224 1 22 HELIX 5 AA5 THR A 230 GLN A 237 1 8 HELIX 6 AA6 PRO A 241 SER A 244 5 4 HELIX 7 AA7 ASP A 245 HIS A 259 1 15 HELIX 8 AA8 GLY A 287 PHE A 300 1 14 HELIX 9 AA9 ASN A 340 VAL A 349 1 10 HELIX 10 AB1 PRO A 371 GLN A 395 1 25 HELIX 11 AB2 SER A 407 VAL A 468 1 62 HELIX 12 AB3 ASP A 473 LYS A 492 1 20 HELIX 13 AB4 LYS A 492 GLU A 512 1 21 HELIX 14 AB5 SER A 522 ASN A 540 1 19 HELIX 15 AB6 ASP A 553 ASP A 557 5 5 HELIX 16 AB7 SER A 572 GLU A 580 1 9 HELIX 17 AB8 PRO A 626 GLN A 632 1 7 HELIX 18 AB9 PRO A 644 MET A 654 1 11 HELIX 19 AC1 ALA A 708 MET A 715 1 8 HELIX 20 AC2 GLU A 716 ILE A 718 5 3 HELIX 21 AC3 SER A 719 GLY A 736 1 18 HELIX 22 AC4 GLY A 770 GLN A 778 1 9 HELIX 23 AC5 GLY A 800 ILE A 804 5 5 HELIX 24 AC6 THR A 810 LEU A 830 1 21 HELIX 25 AC7 ALA A 832 LEU A 836 5 5 HELIX 26 AC8 SER B 317 SER B 325 1 9 HELIX 27 AC9 THR B 329 LEU B 363 1 35 HELIX 28 AD1 ILE B 367 ARG B 371 5 5 HELIX 29 AD2 THR B 384 GLY B 399 1 16 HELIX 30 AD3 ASP B 401 GLY B 410 1 10 HELIX 31 AD4 SER B 413 TYR B 424 1 12 HELIX 32 AD5 ASN B 429 ALA B 439 1 11 SHEET 1 AA1 5 ILE A 584 LYS A 585 0 SHEET 2 AA1 5 ASP A 303 LEU A 307 1 N LEU A 306 O LYS A 585 SHEET 3 AA1 5 LYS A 280 ILE A 284 1 N ILE A 283 O LEU A 307 SHEET 4 AA1 5 ALA A 620 CYS A 623 1 O LEU A 622 N ILE A 284 SHEET 5 AA1 5 LEU A 796 PHE A 798 1 O PHE A 797 N CYS A 623 SHEET 1 AA2 2 THR A 319 LYS A 322 0 SHEET 2 AA2 2 TYR A 325 ASP A 328 -1 O ALA A 327 N PHE A 320 SHEET 1 AA3 3 VAL A 333 VAL A 334 0 SHEET 2 AA3 3 LEU A 565 VAL A 567 -1 O LEU A 565 N VAL A 334 SHEET 3 AA3 3 LEU A 353 LYS A 355 -1 N ALA A 354 O THR A 566 SHEET 1 AA4 4 SER A 609 CYS A 618 0 SHEET 2 AA4 4 GLY A 599 ASN A 606 -1 N VAL A 602 O TYR A 616 SHEET 3 AA4 4 THR A 588 THR A 596 -1 N ARG A 591 O ILE A 603 SHEET 4 AA4 4 GLN A 638 VAL A 640 1 O VAL A 640 N VAL A 593 SHEET 1 AA5 2 GLY A 655 PHE A 656 0 SHEET 2 AA5 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 SHEET 1 AA6 5 LEU A 677 GLY A 679 0 SHEET 2 AA6 5 LEU A 693 TRP A 695 -1 O PHE A 694 N PHE A 678 SHEET 3 AA6 5 ILE A 702 VAL A 707 -1 O LEU A 706 N LEU A 693 SHEET 4 AA6 5 ASN A 660 CYS A 665 -1 N ASN A 660 O VAL A 707 SHEET 5 AA6 5 THR A 746 VAL A 748 -1 O VAL A 747 N VAL A 663 CISPEP 1 ALA A 240 PRO A 241 0 1.46 CISPEP 2 PRO A 470 PRO A 471 0 5.90 CISPEP 3 GLN A 633 PRO A 634 0 2.46 CISPEP 4 VAL A 640 PRO A 641 0 -2.17 SITE 1 AC1 35 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC1 35 GLU A 308 ALA A 309 ARG A 310 GLY A 314 SITE 3 AC1 35 GLY A 315 ARG A 316 VAL A 317 LEU A 329 SITE 4 AC1 35 GLY A 330 ALA A 331 MET A 332 VAL A 333 SITE 5 AC1 35 THR A 588 VAL A 590 THR A 624 LEU A 625 SITE 6 AC1 35 PRO A 626 VAL A 637 TRP A 751 TRP A 756 SITE 7 AC1 35 SER A 760 TYR A 761 GLY A 800 GLU A 801 SITE 8 AC1 35 THR A 810 VAL A 811 ALA A 814 HOH A1003 SITE 9 AC1 35 HOH A1004 HOH A1011 HOH A1015 SITE 1 AC2 3 TRP A 751 ASP A 754 SO4 A 903 SITE 1 AC3 3 ARG A 310 ARG A 312 SO4 A 902 SITE 1 AC4 3 LYS A 374 SER A 522 ARG A 524 SITE 1 AC5 3 SER A 687 GLU A 690 LEU B 389 SITE 1 AC6 2 THR A 189 SER A 190 SITE 1 AC7 5 GLY A 409 GLU A 413 ARG A 526 PHE A 533 SITE 2 AC7 5 ARG A 688 CRYST1 121.073 178.411 234.676 90.00 90.00 90.00 I 2 2 2 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 0.008259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004261 0.00000