SMTL ID : 2h0v.1

Crystal structure of a putative quercetin 2,3-dioxygenase (yxag, bsu39980) from bacillus subtilis at 2.60 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: H.63, H.65, E.70, H.104 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.63, A:H.65, A:E.70, A:H.104 FE.2: 5 residues within 4Å: Chain A: H.235, H.237, E.242, H.276 Ligands: TLA.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.235, A:H.237, A:E.242, A:H.276 FE.13: 5 residues within 4Å: Chain B: H.63, H.65, E.70, H.104 Ligands: EDO.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.63, B:H.65, B:E.70, B:H.104 FE.14: 5 residues within 4Å: Chain B: H.235, H.237, E.242, H.276 Ligands: TLA.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.235, B:H.237, B:E.242, B:H.276

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: H.63, H.65, E.70, H.104, Y.128 Ligands: FE.1 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: L.28, F.29, G.30, I.131, N.133, E.146, E.147, V.148, R.152 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: E.225, E.248, Y.284, K.286 Chain B: D.76, R.112 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: E.248 Chain B: R.112, P.264 Ligands: EDO.21 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: K.56, K.78 Chain B: L.176, A.177, E.178, E.192 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: H.283 Chain B: G.22, R.26, D.136 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: D.76, G.77, I.91, S.92 Chain B: S.92 Ligands: EDO.18 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: L.75, R.114, Y.245, C.246, L.247, G.265 Ligands: EDO.24 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: H.63, H.65, E.70, H.104, Y.128 Ligands: FE.13 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: S.92 Chain B: D.76, G.77, I.91, S.92 Ligands: EDO.11 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: L.28, F.29, G.30, I.131, N.133, E.146, R.152 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: G.196, D.197, R.198, Y.307, E.308 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: L.75, R.114, Y.245, C.246, L.247, G.265 Ligands: EDO.8 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: E.80, L.81, T.82, R.87, S.105, Y.106, R.107, E.167 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: L.89, A.174, L.176 Chain B: L.89, A.174, L.176 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: S.21, R.112, R.114, P.264 Chain B: E.248 Ligands: EDO.12 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: L.176 Chain B: K.56, K.78, Q.109 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: D.197, K.213, R.301 Ligand excluded by PLIP

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.4: 12 residues within 4Å: Chain A: I.232, H.235, H.237, E.242, F.244, H.276, Y.278, L.291, P.298, F.299, F.300 Ligands: FE.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.299, A:F.300 Water bridges: A:H.206, A:Y.278 Salt bridges: A:H.235, A:H.276 TLA.16: 11 residues within 4Å: Chain B: I.232, H.235, H.237, E.242, F.244, H.276, Y.278, P.298, F.299, F.300 Ligands: FE.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.299, B:F.300 Salt bridges: B:H.235, B:H.276

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 7 residues within 4Å: Chain A: R.31, K.56, P.142, Y.143 Chain B: E.308, G.309, H.310 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:H.310, A:R.31, A:R.31, A:K.56, A:P.142 Water bridges: A:K.56 TRS.17: 7 residues within 4Å: Chain A: E.308, G.309, H.310 Chain B: R.31, K.56, P.142, Y.143 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:H.310, A:H.310, B:R.31, B:K.56, B:Y.143, B:Y.143 Water bridges: B:K.56, B:H.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of (2636545) from Bacillus subtilis at 2.60 A resolution. To be published

Release Date

2006-05-30

Peptides

Quercetin 2,3-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Quercetin 2,3-dioxygenase