SMTL ID : 3o2g.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.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.14 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.10: 4 residues within 4Å: Chain B: H.203, D.205, H.348 Ligands: OGA.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.203, B:D.205, B:H.348, H2O.31 ZN.11: 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: 11 residues within 4Å: Chain A: V.184, A.194, L.200, H.203, D.205, H.348, R.350, R.361, L.363 Ligands: ZN.1, NM2.4 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.203, A:R.350, A:R.361 OGA.12: 11 residues within 4Å: Chain B: V.184, A.194, L.200, H.203, D.205, H.348, R.350, R.361, L.363 Ligands: ZN.10, NM2.13 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.203, B:R.350, B:R.361

2 x NM2: 3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM(Non-covalent)

NM2.4: 12 residues within 4Å: Chain A: Y.178, W.182, N.192, A.194, Y.195, D.205, Y.206, P.207, N.293, T.296, Y.367 Ligands: OGA.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.192, A:N.192, A:Y.206, A:N.293 Salt bridges: A:D.205 pi-Cation interactions: A:Y.178, A:W.182, A:W.182 NM2.13: 12 residues within 4Å: Chain B: Y.178, W.182, N.192, A.194, Y.195, D.205, Y.206, P.207, N.293, T.296, Y.367 Ligands: OGA.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.192, B:N.192, B:Y.206, B:N.293, 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

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

EDO.5: 1 residues within 4Å: Chain A: K.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.275 Water bridges: A:K.275 EDO.6: 5 residues within 4Å: Chain A: W.117, G.118, E.120, N.237, K.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.120, A:N.237, A:K.241, A:K.241 EDO.7: 4 residues within 4Å: Chain A: K.99, R.102 Chain B: D.302, P.304 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.302, A:K.99, A:R.102, A:R.102 EDO.8: 6 residues within 4Å: Chain A: C.239, Q.240, F.250, G.285, Q.286, V.287 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.239, A:G.285, A:V.287 Water bridges: A:Q.240 EDO.9: 3 residues within 4Å: Chain A: Q.115, L.121, Q.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.122 EDO.14: 1 residues within 4Å: Chain B: K.275 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.275 Water bridges: B:K.275 EDO.15: 5 residues within 4Å: Chain B: W.117, G.118, E.120, N.237, K.241 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.120, B:N.237, B:K.241, B:K.241 EDO.16: 4 residues within 4Å: Chain A: D.302, P.304 Chain B: K.99, R.102 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.99, B:R.102, B:R.102, A:D.302 EDO.17: 6 residues within 4Å: Chain B: C.239, Q.240, F.250, G.285, Q.286, V.287 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.239, B:G.285, B:V.287 Water bridges: B:Q.240 EDO.18: 3 residues within 4Å: Chain B: Q.115, L.121, Q.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.122

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

2010-09-15

Peptides

Gamma-butyrobetaine dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Gamma-butyrobetaine dioxygenase

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