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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF COMPOUND 3 (4-HYDROXY-6-[2-(7-HYDROXY-2-OXO-4-PHENYL-2H-CHROMEN-6-YL)ETHYL]PYRIDAZIN-3(2H)-ONE) AND FAD BOUND TO HUMAN DAAO AT 2.4A
 
Authors :  C. M. Lukacs, L. Chun
Date :  20 May 14  (Deposition) - 16 Jul 14  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidase, Oxidoreductase, Daao, D-Amino Acid Oxidase, Fad Dependent, Nmdar, Schizophrenia, D-Serine Competitive, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Terry-Lorenzo, L. E. Chun, S. P. Brown, M. L. Heffernan, Q. K. Fang M. A. Orsini, L. Pollegioni, L. W. Hardy, K. L. Spear, T. H. Large
Novel Human D-Amino Acid Oxidase Inhibitors Stabilize An Active-Site Lid-Open Conformation.
Biosci. Rep. V. 34 2014
PubMed-ID: 25001371  |  Reference-DOI: 10.1042/BSR20140071

(-) Compounds

Molecule 1 - D-AMINO-ACID OXIDASE
    Chains: A, B
    EC Number: 1.4.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DAMOX, DAO, DAO DAMOX
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DAAO, DAMOX, DAO

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
131T2Ligand/Ion4-HYDROXY-6-[2-(7-HYDROXY-2-OXO-4-PHENYL-2H-CHROMEN-6-YL)ETHYL]PYRIDAZIN-3(2H)-ONE
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3K1Ligand/IonPOTASSIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , ALA A:8 , GLY A:9 , VAL A:10 , ILE A:11 , ALA A:36 , ASP A:37 , ARG A:38 , THR A:43 , THR A:44 , THR A:45 , VAL A:47 , ALA A:48 , GLY A:50 , LEU A:51 , ARG A:162 , LYS A:163 , VAL A:164 , CYS A:181 , THR A:182 , GLY A:183 , TRP A:185 , ILE A:202 , ARG A:283 , GLY A:312 , GLY A:313 , TYR A:314 , GLY A:315 , LEU A:316 , THR A:317 , 31T A:402 , HOH A:501 , HOH A:504 , HOH A:507 , HOH A:508 , HOH A:538BINDING SITE FOR RESIDUE FAD A 401
2AC2SOFTWAREGLN A:53 , TYR A:55 , LEU A:56 , LEU A:215 , TYR A:224 , SER A:226 , TYR A:228 , ILE A:230 , GLY A:240 , ARG A:283 , GLY A:313 , FAD A:401 , HOH A:557BINDING SITE FOR RESIDUE 31T A 402
3AC3SOFTWARELEU B:122 , PHE B:125 , TYR B:128BINDING SITE FOR RESIDUE K B 401
4AC4SOFTWAREGLY B:7 , ALA B:8 , GLY B:9 , VAL B:10 , ILE B:11 , ALA B:36 , ASP B:37 , ARG B:38 , THR B:44 , THR B:45 , VAL B:47 , ALA B:48 , GLY B:50 , LEU B:51 , ARG B:162 , LYS B:163 , VAL B:164 , CYS B:181 , THR B:182 , GLY B:183 , TRP B:185 , TYR B:228 , GLY B:281 , ARG B:283 , HIS B:311 , GLY B:312 , GLY B:313 , TYR B:314 , GLY B:315 , LEU B:316 , THR B:317 , 31T B:403 , HOH B:502 , HOH B:504 , HOH B:505 , HOH B:522BINDING SITE FOR RESIDUE FAD B 402
5AC5SOFTWARELEU B:51 , GLN B:53 , TYR B:55 , LEU B:56 , LEU B:215 , TYR B:224 , TYR B:228 , ARG B:283 , GLY B:313 , FAD B:402BINDING SITE FOR RESIDUE 31T B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QFC)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gln A:28 -Pro A:29
2Thr A:40 -Pro A:41
3Thr B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QFC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QFC)

(-) Exons   (0, 0)

(no "Exon" information available for 4QFC)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh......eeeeee.......hhhhh............hhhhhhhhhhhhhhhhhhh...hhhhhheeeeeeeeee.............eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhh..eeee....hhhhhhhh...eeee.hhhhhhhh......eeeeeeeeeee.....eeeee.......eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....eeeeeee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qfc A   1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDIYNSPYIIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEK 337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       224       234       244       254       264       274       284       294   ||  307       317       327       337
                                                                                                                                                                                                                                                   218|                                                                        298|                                   
                                                                                                                                                                                                                                                    223                                                                         302                                   


Chain B from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh...eeeeee.......hhhhh...........hhhhhhhhhhhhhhh.....hhhhhheeeeeeeeee.............eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhh..eeee....hhhhhhhh...eeee.hhhhhhhh......eeeeeeeeeee.....eeeee.........eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....eeeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfc B   1 MRVVVIGAGVIGLSTALCIHERYHSPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPGIYNSPYIIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEK 337
                                    10        20    ||  33        43        53    ||  66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216  ||   228       238       248       258       268       278       288       304       314       324       334   
                                                   25|                           58|                                                                                                                                                          219|                                                                       296|                                  
                                                    29                            62                                                                                                                                                           222                                                                        303
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4QFC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QFC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QFC)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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        OXDA_HUMAN | P14920: 2du8 2e48 2e49 2e4a 2e82 2gnz 3cuk 3g3e 3w4i 3w4j 3w4k 3znn 3zno 3znp 3znq 4qfd

(-) Related Entries Specified in the PDB File

4qfd DAAO BOUND TO SEP0374036