SMTL ID : 5hv0.1

Structural Analysis of Cofactor Binding of a Prolyl 4-Hydroxylase from the Pathogenic Bacterium Bacillus anthracis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

14 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: H.128, D.130, H.194 Ligands: AKG.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.128, A:D.130, A:D.130, A:H.194 CD.2: 1 residues within 4Å: Chain A: E.91 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.91, A:E.91, H2O.6 CD.3: 1 residues within 4Å: Chain A: E.52 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.52, A:E.52 CD.4: 1 residues within 4Å: Chain A: N.105 No protein-ligand interaction detected (PLIP) CD.5: 1 residues within 4Å: Chain A: H.19 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.19, H2O.1, H2O.6, H2O.7, H2O.8 CD.6: 2 residues within 4Å: Chain A: E.120, G.202 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.120, A:E.120 CD.7: 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.8: 1 residues within 4Å: Chain A: E.155 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.155, A:E.155 CD.9: 1 residues within 4Å: Chain A: H.135 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.135, H2O.7 CD.13: 4 residues within 4Å: Chain B: H.128, D.130, H.194 Ligands: AKG.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.128, B:D.130, B:D.130, B:H.194 CD.14: 1 residues within 4Å: Chain B: H.19 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.19, H2O.9, H2O.13, H2O.14, H2O.15 CD.15: 2 residues within 4Å: Chain B: G.84, H.115 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.115, H2O.15, H2O.17 CD.16: 2 residues within 4Å: Chain B: E.120, E.203 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.120, B:E.120, B:E.203, H2O.10 CD.17: 1 residues within 4Å: Chain B: H.135 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.135, H2O.15

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

AKG.10: 13 residues within 4Å: Chain A: Y.119, Y.125, H.128, D.130, V.148, T.160, H.194, G.196, K.204, I.206, T.208, W.210 Ligands: CD.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.125, A:I.206 Hydrogen bonds: A:T.160 Salt bridges: A:K.204 AKG.18: 13 residues within 4Å: Chain B: Y.119, Y.125, H.128, D.130, V.148, 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:V.148, B:I.206 Hydrogen bonds: B:Y.119, B:Y.119 Water bridges: B:T.208, B:T.208 Salt bridges: B:K.204

1 x K: POTASSIUM ION(Non-covalent)

K.11: 3 residues within 4Å: Chain A: T.81, S.83, H.115 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.81, A:S.83, A:H.115, H2O.6, H2O.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 3 residues within 4Å: Chain A: S.50, D.51, E.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.50, A:S.50, A:E.52 GOL.19: 5 residues within 4Å: Chain A: M.175 Chain B: Q.32, G.46, N.47, M.175 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.32, B:Q.32, B:N.47 Water bridges: B:N.47

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

Prolyl 4-Hydroxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prolyl 4-Hydroxylase

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