SMTL ID : 3gkv.1

X-ray structure of an intermediate along the oxidation pathway of Trematomus bernacchii hemoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: M.33, T.40, Y.43, F.44, H.46, W.47, H.60, K.63, V.64, I.68, L.85, Q.88, H.89, L.93, V.95, N.99, F.100, L.103, N.104, L.138 Ligands: CMO.2 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Y.43, A:F.44, A:V.64, A:I.68, A:L.85, A:L.93, A:L.93, A:V.95, A:V.95, A:L.138 Hydrogen bonds: A:Q.88 Water bridges: A:H.60, A:H.60, A:K.63 Salt bridges: A:H.46, A:H.60, A:K.63, A:K.63 pi-Stacking: A:H.60 Metal complexes: A:H.89, H2O.6 HEM.3: 17 residues within 4Å: Chain B: T.38, H.41, F.42, H.63, K.66, V.67, G.70, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.4 16 PLIP interactions: 15 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.42, B:F.42, B:K.66, B:V.67, B:L.88, B:L.91, B:L.96, B:V.98, B:V.98, B:L.106, B:L.141 Salt bridges: B:H.63, B:K.66, B:K.66 Metal complexes: B:H.92, CMO.4 HEM.5: 21 residues within 4Å: Chain C: M.33, T.40, Y.43, F.44, H.46, W.47, H.60, K.63, V.64, I.68, L.85, Q.88, H.89, L.93, V.95, N.99, F.100, L.103, N.104, L.138 Ligands: CMO.6 19 PLIP interactions: 18 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:Y.43, C:F.44, C:V.64, C:I.68, C:L.85, C:L.93, C:L.93, C:V.95, C:V.95, C:L.138 Hydrogen bonds: C:Q.88 Water bridges: C:K.63 Salt bridges: C:H.46, C:H.60, C:K.63, C:K.63 pi-Stacking: C:H.60 Metal complexes: C:H.89, H2O.15 HEM.7: 17 residues within 4Å: Chain D: T.38, H.41, F.42, H.63, K.66, V.67, G.70, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.8 16 PLIP interactions: 15 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.42, D:F.42, D:K.66, D:V.67, D:L.88, D:L.91, D:L.96, D:V.98, D:V.98, D:L.106, D:L.141 Salt bridges: D:H.63, D:K.66, D:K.66 Metal complexes: D:H.92, CMO.8

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.2: 5 residues within 4Å: Chain A: L.30, H.60, V.64, H.89 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CMO.4: 4 residues within 4Å: Chain B: H.63, V.67, H.92 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.63 CMO.6: 5 residues within 4Å: Chain C: L.30, H.60, V.64, H.89 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) CMO.8: 4 residues within 4Å: Chain D: H.63, V.67, H.92 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Merlino, A. et al., Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins. Biopolymers (2009)

Release Date

2009-05-05

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin subunit alpha

Hemoglobin subunit beta

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