SMTL ID : 1h1m.1 (1 other biounit)

CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 8 residues within 4Å: Chain A: V.190, N.191 Chain B: L.61, Q.83, T.184, T.187, D.188, T.189 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.161 Hydrogen bonds: B:T.189

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 8 residues within 4Å: Chain A: Q.83, T.184, R.186, T.187, D.188, T.189 Chain B: V.190, N.191 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.185 Hydrogen bonds: A:T.189

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: Q.69, R.108, N.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.69, A:N.109 NAG.4: 4 residues within 4Å: Chain A: N.248, G.272, S.325, G.326 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.248 Water bridges: A:P.271, A:A.273, A:S.325, A:S.325, A:S.327 NAG.5: 1 residues within 4Å: Chain A: N.90 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: T.141, N.142 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain B: Q.69, R.108, N.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.109 Water bridges: B:Q.69 NAG.11: 5 residues within 4Å: Chain B: N.248, P.271, G.272, S.325, G.326 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.248 Water bridges: B:N.248, B:A.273, B:S.325, B:S.325, B:S.325, B:S.325 NAG.12: 3 residues within 4Å: Chain B: R.26, Y.137, N.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.142 Water bridges: B:N.142

2 x KMP: 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE(Non-covalent)

KMP.7: 21 residues within 4Å: Chain A: V.30, Y.35, M.51, T.53, V.63, H.66, H.68, E.73, F.75, H.112, F.114, M.123, G.125, F.132, L.135, F.136, L.139, G.163, P.164, V.177 Ligands: CU.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.35, A:F.75, A:F.75, A:F.114, A:F.136, A:F.136, A:L.139, A:P.164 Hydrogen bonds: A:Y.35 Water bridges: A:M.123, A:G.125 pi-Stacking: A:F.136 KMP.13: 19 residues within 4Å: Chain B: Y.35, M.51, T.53, V.63, H.66, H.68, E.73, F.75, F.114, M.123, G.125, F.132, L.135, F.136, L.139, G.163, P.164, V.177 Ligands: CU.14 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.35, B:E.73, B:F.75, B:F.75, B:F.114, B:L.135, B:L.139 Water bridges: B:Y.35, B:M.123, B:G.125 pi-Stacking: B:F.136, B:F.136

2 x CU: COPPER (II) ION(Non-covalent)

CU.8: 5 residues within 4Å: Chain A: H.66, H.68, E.73, H.112 Ligands: KMP.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.66, A:H.68, A:E.73, A:H.112 CU.14: 5 residues within 4Å: Chain B: H.66, H.68, E.73, H.112 Ligands: KMP.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.66, B:H.68, B:E.73, B:H.112

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.9: 11 residues within 4Å: Chain A: V.97, S.99, D.102, N.191, W.200, H.201 Chain B: S.81, V.97, Q.117, D.118 Ligands: MPD.15 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.97 Hydrogen bonds: B:Q.117, B:Q.117, A:S.99, A:S.99 MPD.15: 10 residues within 4Å: Chain A: S.81, V.97, Q.117, D.118 Chain B: V.97, S.99, D.102, W.200, H.201 Ligands: MPD.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.97 Hydrogen bonds: A:Q.117, B:S.99, B:S.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steiner, R.A. et al., Anaerobic Enzyme.Substrate Structures Provide Insight Into the Reaction Mechanism of the Copper- Dependent Quercetin 2,3-Dioxygenase. Proc.Natl.Acad.Sci.USA (2002)

Release Date

2002-11-28

Peptides

QUERCETIN 2,3-DIOXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

QUERCETIN 2,3-DIOXYGENASE

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