SMTL ID : 3ms5.1

Crystal Structure of Human gamma-butyrobetaine,2-oxoglutarate dioxygenase 1 (BBOX1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.203, D.205, H.348 Ligands: OGA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.203, A:D.205, A:H.348, H2O.16 NI.14: 4 residues within 4Å: Chain B: H.203, D.205, H.348 Ligands: OGA.16 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.203, B:D.205, B:H.348, H2O.32

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.39, C.41, C.44, H.83 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.39, A:C.41, A:C.44, A:H.83 ZN.15: 4 residues within 4Å: Chain B: C.39, C.41, C.44, H.83 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.39, B:C.41, B:C.44, B:H.83

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.3: 13 residues within 4Å: Chain A: V.184, A.194, L.200, H.203, D.205, H.348, R.350, R.361, L.363 Ligands: NI.1, REE.4, EDO.6, EDO.8 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.203, A:R.350, A:R.361 OGA.16: 13 residues within 4Å: Chain B: V.184, A.194, L.200, H.203, D.205, H.348, R.350, R.361, L.363 Ligands: NI.14, REE.17, EDO.19, EDO.21 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.203, B:R.350, B:R.361

2 x REE: 2-(2-carboxyethyl)-1,1,1-trimethyldiazanium(Non-covalent)

REE.4: 12 residues within 4Å: Chain A: Y.178, W.182, N.192, Y.195, D.205, Y.206, P.207, N.293, T.296, Y.367 Ligands: OGA.3, EDO.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.205 Hydrogen bonds: A:N.192, A:Y.206, A:N.293, A:Y.367 Salt bridges: A:D.205 pi-Cation interactions: A:Y.178, A:W.182, A:W.182 REE.17: 12 residues within 4Å: Chain B: Y.178, W.182, N.192, Y.195, D.205, Y.206, P.207, N.293, T.296, Y.367 Ligands: OGA.16, EDO.19 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:D.205 Hydrogen bonds: B:N.192, B:Y.206, B:N.293, B:Y.367, B:Y.367 Water bridges: B:T.296, B:T.296 Salt bridges: B:D.205 pi-Cation interactions: B:Y.178, B:W.182, B:W.182

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

EDO.5: 5 residues within 4Å: Chain A: E.280, V.288, R.289, W.344 Chain B: H.210 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: N.192, A.194, L.200, H.203, N.293, A.295 Ligands: OGA.3, REE.4 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: K.199, L.200, S.201, H.203, N.293, A.295 Chain B: L.55 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: L.218, S.230, E.231, I.339, H.348, G.349 Ligands: OGA.3 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Y.174, L.175 Chain B: Y.174, L.175 Ligands: EDO.22 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain A: T.261, A.295, R.297, D.298, T.299 Chain B: Y.45, K.50, A.51, R.52 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: K.146, D.342, W.370 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Q.240, F.250, G.285, Q.286, V.287 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: W.34, R.95, C.96, F.97, R.102 Chain B: T.299, I.300, F.301, D.302 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: H.210 Chain B: E.280, V.288, R.289, W.344 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain B: N.192, A.194, L.200, H.203, N.293, A.295 Ligands: OGA.16, REE.17 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: L.55 Chain B: K.199, L.200, S.201, H.203, N.293, A.295 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: L.218, S.230, E.231, I.339, H.348, G.349 Ligands: OGA.16 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: Y.174, L.175 Chain B: Y.174, L.175 Ligands: EDO.9 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain A: Y.45, K.50, A.51, R.52 Chain B: T.261, A.295, R.297, D.298, T.299 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: K.146, D.342, W.370 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: Q.240, F.250, G.285, Q.286, V.287 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain A: T.299, I.300, F.301, D.302 Chain B: W.34, R.95, C.96, F.97, R.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leung, I.K. et al., Structural and mechanistic studies on gamma-butyrobetaine hydroxylase. Chem. Biol. (2010)

Release Date

2010-05-12

Peptides

Gamma-butyrobetaine dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Gamma-butyrobetaine dioxygenase

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