SMTL ID : 5hv4.1

Crystal Structure of a Prolyl 4-Hydroxylase Complexed with Alpha-ketoglutarate from the Pathogenic Bacterium Bacillus anthracis in C2221

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

10 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: H.128, D.130, H.194 Ligands: AKG.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.128, A:D.130, A:H.194 CD.2: 2 residues within 4Å: Chain A: D.18, N.105 No protein-ligand interaction detected (PLIP) CD.3: 1 residues within 4Å: Chain A: H.19 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.19, H2O.3, H2O.4 CD.4: 1 residues within 4Å: Chain A: D.122 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.122, A:D.122 CD.5: 1 residues within 4Å: Chain A: E.56 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.56, A:E.56 CD.13: 4 residues within 4Å: Chain B: H.128, D.130, H.194 Ligands: AKG.18 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.128, B:D.130, B:H.194 CD.14: 2 residues within 4Å: Chain B: D.18, N.105 No protein-ligand interaction detected (PLIP) CD.15: 1 residues within 4Å: Chain B: H.19 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.19, H2O.7, H2O.8 CD.16: 1 residues within 4Å: Chain B: D.122 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.122, B:D.122 CD.17: 1 residues within 4Å: Chain B: E.56 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.56, B:E.56

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.6: 11 residues within 4Å: Chain A: Y.119, Y.125, H.128, T.160, H.194, G.196, K.204, I.206, T.208, W.210 Ligands: CD.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.160, A:I.206 Hydrogen bonds: A:D.130, A:T.160, A:T.208 Salt bridges: A:K.204 AKG.18: 11 residues within 4Å: Chain B: Y.119, Y.125, H.128, T.160, H.194, G.196, K.204, I.206, T.208, W.210 Ligands: CD.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.160, B:I.206 Hydrogen bonds: B:Y.119, B:D.130, B:T.160 Water bridges: B:T.208 Salt bridges: B:K.204

12 x K: POTASSIUM ION(Non-covalent)

K.7: 2 residues within 4Å: Chain A: D.55, K.173 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.55 K.8: 2 residues within 4Å: Chain A: D.185, S.187 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.185, A:S.187 K.9: 1 residues within 4Å: Chain A: H.115 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.115 K.10: 2 residues within 4Å: Chain A: E.120, E.203 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.120, A:E.203, H2O.1 K.11: 1 residues within 4Å: Chain A: E.155 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.155, H2O.1 K.12: 1 residues within 4Å: Chain A: H.135 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.135 K.19: 2 residues within 4Å: Chain B: D.55, K.173 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.55 K.20: 2 residues within 4Å: Chain B: D.185, S.187 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.185, B:S.187 K.21: 1 residues within 4Å: Chain B: H.115 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.115 K.22: 2 residues within 4Å: Chain B: E.120, E.203 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.120, B:E.203, H2O.5 K.23: 1 residues within 4Å: Chain B: E.155 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.155, H2O.5 K.24: 1 residues within 4Å: Chain B: H.135 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schnicker, N.J. et al., Structural analysis of cofactor binding for a prolyl 4-hydroxylase from the pathogenic bacterium Bacillus anthracis. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-05-04

Peptides

2OG-Fe(II) oxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

2OG-Fe(II) oxygenase

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