SMTL ID : 1v4u.1

Crystal structure of bluefin tuna carbonmonoxy-hemoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-oligomer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: M.34, Y.44, F.45, H.47, W.48, H.61, K.64, V.65, L.86, L.89, H.90, M.94, V.96, N.100, F.101, L.104, V.135, L.139 Ligands: CMO.2 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.44, A:F.45, A:F.45, A:F.45, A:L.86, A:V.96, A:V.135, A:L.139 Hydrogen bonds: A:W.48 Salt bridges: A:H.47, A:H.61 pi-Cation interactions: A:H.90 Metal complexes: A:H.90, CMO.2 HEM.3: 17 residues within 4Å: Chain B: T.38, Y.41, F.42, Y.45, H.63, K.66, V.67, G.70, L.71, L.88, H.92, 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:T.38, B:Y.41, B:Y.41, B:F.42, B:V.67, B:V.67, B:L.71, B:L.88, B:V.98, B:N.102, B:L.106, B:L.141 Hydrogen bonds: B:Y.45 pi-Stacking: B:H.63 Metal complexes: B:H.92, CMO.4 HEM.5: 19 residues within 4Å: Chain C: M.34, Y.44, F.45, H.47, W.48, H.61, K.64, V.65, L.86, L.89, H.90, M.94, V.96, N.100, F.101, L.104, V.135, L.139 Ligands: CMO.6 17 PLIP interactions: 16 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.44, C:Y.44, C:F.45, C:F.45, C:F.45, C:L.86, C:V.96, C:L.104, C:V.135, C:L.139 Hydrogen bonds: C:W.48 Salt bridges: C:H.47, C:H.61, C:K.64 pi-Stacking: C:H.90 Metal complexes: C:H.90, CMO.6 HEM.7: 18 residues within 4Å: Chain D: T.38, Y.41, F.42, Y.45, H.63, K.66, V.67, G.70, L.71, L.88, L.91, H.92, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.8 15 PLIP interactions: 14 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.41, D:Y.41, D:F.42, D:K.66, D:V.67, D:L.71, D:L.88, D:N.102, D:F.103, D:L.106, D:L.141 Hydrogen bonds: D:Y.45, D:Y.45 Metal complexes: D:H.92, CMO.8

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

CMO.2: 5 residues within 4Å: Chain A: F.45, H.61, V.65, H.90 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.61 CMO.4: 5 residues within 4Å: Chain B: F.42, 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: F.45, H.61, V.65, H.90 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.61 CMO.8: 4 residues within 4Å: Chain D: H.63, V.67, H.92 Ligands: HEM.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., Novel Mechanisms of pH Sensitivity in Tuna Hemoglobin: A STRUCTURAL EXPLANATION OF THE ROOT EFFECT. J.Biol.Chem. (2004)

Release Date

2004-07-06

Peptides

hemoglobin alpha chain: AC
hemoglobin beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

hemoglobin alpha chain

hemoglobin beta chain

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