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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF COMPOUND 2 (3-(7-HYDROXY-2-OXO-4-PHENYL-2H-CHROMEN-6-YL)PROPANOIC ACID) AND FAD BOUND TO HUMAN DAAO AT 2.85A
 
Authors :  T. E. Edwards, L. Chun, T. L. Arakaki
Date :  20 May 14  (Deposition) - 16 Jul 14  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Oxidase, Oxidoreductase, Daao, D-Amino Acid Oxidase, D-Serine Competitive, Schizophrenia, Nmda Receptor, 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
    Expression System Vector Type: PLASMID
    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 Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
131R2Ligand/Ion3-(7-HYDROXY-2-OXO-4-PHENYL-2H-CHROMEN-6-YL)PROPANOICACID
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3NA2Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
131R2Ligand/Ion3-(7-HYDROXY-2-OXO-4-PHENYL-2H-CHROMEN-6-YL)PROPANOICACID
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
131R2Ligand/Ion3-(7-HYDROXY-2-OXO-4-PHENYL-2H-CHROMEN-6-YL)PROPANOICACID
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3NA-1Ligand/IonSODIUM ION
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
131R4Ligand/Ion3-(7-HYDROXY-2-OXO-4-PHENYL-2H-CHROMEN-6-YL)PROPANOICACID
2FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:122 , PHE A:125 , PRO A:126 , TYR A:128BINDING SITE FOR RESIDUE NA A 401
2AC2SOFTWAREGLY 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:44 , THR A:45 , VAL A:47 , ALA A:48 , ALA A:49 , GLY A:50 , LEU A:51 , ARG A:162 , VAL A:164 , CYS A:181 , THR A:182 , GLY A:183 , TRP A:185 , GLY A:281 , ARG A:283 , GLY A:312 , GLY A:313 , TYR A:314 , GLY A:315 , LEU A:316 , THR A:317 , 31R A:403 , HOH A:503 , HOH A:504 , HOH A:505BINDING SITE FOR RESIDUE FAD A 402
3AC3SOFTWAREGLN A:53 , PRO A:54 , TYR A:55 , LEU A:56 , THR A:216 , HIS A:217 , TYR A:224 , SER A:226 , TYR A:228 , ARG A:283 , GLY A:313 , FAD A:402 , HOH A:508BINDING SITE FOR RESIDUE 31R A 403
4AC4SOFTWARELEU B:122 , PHE B:125 , PRO B:126 , TYR B:128BINDING SITE FOR RESIDUE NA B 401
5AC5SOFTWAREGLY 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 , ALA B:48 , ALA B:49 , GLY B:50 , LEU B:51 , ARG B:162 , VAL B:164 , THR B:182 , GLY B:183 , TRP B:185 , ILE B:202 , GLY B:281 , ARG B:283 , GLY B:312 , GLY B:313 , TYR B:314 , GLY B:315 , LEU B:316 , THR B:317 , 31R B:403BINDING SITE FOR RESIDUE FAD B 402
6AC6SOFTWAREGLN B:53 , PRO B:54 , TYR B:55 , TYR B:224 , SER B:226 , TYR B:228 , ARG B:283 , GLY B:313 , FAD B:402BINDING SITE FOR RESIDUE 31R B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:40 -Pro A:41
2Thr B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QFD)

(-) Sequences/Alignments

Asymmetric 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:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeeee......hhhhhh.........hhhhhhhhhhhhhhhhh...hhhhhheeeeeeeeee......hhhhhh.eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh.eeee.hhhhhhhhh.....eeeeeeeeeee......eeee.hhhhh.....eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....eeeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfd A   1 MRVVVIGAGVIGLSTALCIHERYHLDIKVYADRFTPLTTTDVAAGLWQPYLPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEE 336
                                    10        20   ||   35        45        55||      70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       304       314       324       334  
                                                  24|                        56|                                                                                                                                                                                                                                         298|                                 
                                                   30                         62                                                                                                                                                                                                                                          303                                 


Chain B from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeeee......hhhhhh.........hhhhhhhhhhhhhhhhh...hhhhhheeeeeeeeee......hhhhhh.eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh.eeee.hhhhhhhhh.....eeeeeeeeeee......eeee.......eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....eeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfd B   1 MRVVVIGAGVIGLSTALCIHERYHLDIKVYADRFTPLTTTDVAAGLWQPYLPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDIYNSPYIIPGTQTVTLGGIFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEE 336
                                    10        20   ||   35        45        55||      70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       224       234       244       254       264       274       284       294||     311       321       331     
                                                  24|                        56|                                                                                                                                                         218|                                                                     295|                                 
                                                   30                         62                                                                                                                                                          223                                                                      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 4QFD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

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

(-) Related Entries Specified in the PDB File

4qfc DAAO BOUND TO SEP0376049