SMTL ID : 5lkv.1

Dehaloperoxidase B from Amphitrite ornata: imidazole complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 17 residues within 4Å: Chain A: F.24, E.31, N.34, F.35, H.55, K.58, V.59, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.127 Ligands: IMD.5 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:F.35, A:V.59, A:L.83, A:Q.88, A:L.92, A:N.96, A:F.97, A:F.97, A:L.127 Water bridges: A:H.55 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89 HEM.7: 19 residues within 4Å: Chain B: F.24, E.31, N.34, F.35, H.55, K.58, V.59, L.62, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.100, L.127 Ligands: IMD.9 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:F.24, B:F.35, B:V.59, B:L.62, B:L.83, B:Q.88, B:L.92, B:F.97, B:L.100, B:L.127 Water bridges: B:N.37 Salt bridges: B:H.55 Metal complexes: B:H.89

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: K.32, V.39, G.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:K.41 Salt bridges: A:K.32 SO4.3: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.2, A:K.3, A:D.116 Water bridges: A:G.1, A:Q.4, A:S.119 SO4.4: 2 residues within 4Å: Chain A: G.95, K.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.95 Water bridges: A:T.93, A:T.93 Salt bridges: A:K.99 SO4.8: 3 residues within 4Å: Chain B: G.1, F.2, K.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.1, B:F.2, B:K.3 Water bridges: B:G.1, B:Q.4, B:S.119

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 4 residues within 4Å: Chain A: F.21, F.35, V.59 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) IMD.9: 4 residues within 4Å: Chain B: F.21, F.35, V.59 Ligands: HEM.7 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: N.26 No protein-ligand interaction detected (PLIP) GOL.10: 6 residues within 4Å: Chain B: Q.4, D.5, T.8, Q.113, S.114, F.115 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.4, B:D.5, B:D.5, B:Q.113, B:S.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chicano, T.M. et al., Dehaloperoxidase B from Amphitrite ornata: imidazole complex. to be published

Release Date

2017-08-16

Peptides

Dehaloperoxidase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase B

Related Entries With Identical Sequence