SMTL ID : 1iwh.1

Crystal Structure of Horse Carbonmonoxyhemoglobin-Bezafibrate Complex at 1.55A Resolution: A Novel Allosteric Binding Site in R-State Hemoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: T.39, Y.42, F.43, F.46, H.58, K.61, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.2, PEM.3 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:F.43, A:K.61, A:K.61, A:L.83, A:L.83, A:L.86, A:L.91, A:V.93, A:F.98, A:F.98, A:L.101, A:L.136 Water bridges: A:H.58, A:K.61, A:K.61, A:K.61, A:K.61, A:K.61 Salt bridges: A:K.61 pi-Stacking: A:H.87 Metal complexes: A:H.87, CMO.2 HEM.4: 19 residues within 4Å: Chain B: T.38, F.41, F.42, F.45, H.63, K.66, V.67, S.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.5 24 PLIP interactions: 23 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:V.67, B:V.67, B:F.71, B:F.71, B:L.88, B:L.91, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Water bridges: B:H.63 Salt bridges: B:H.63, B:K.66 pi-Stacking: B:H.92, B:H.92 Metal complexes: B:H.92, CMO.5 HEM.6: 18 residues within 4Å: Chain C: T.39, Y.42, F.43, F.46, H.58, K.61, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.7, PEM.8 25 PLIP interactions: 24 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.42, C:Y.42, C:Y.42, C:F.43, C:F.43, C:K.61, C:K.61, C:L.83, C:L.83, C:L.86, C:L.91, C:V.93, C:F.98, C:F.98, C:L.101, C:L.136 Water bridges: C:K.61, C:K.61, C:K.61, C:K.61, C:K.61 Salt bridges: C:K.61 pi-Stacking: C:H.87 Metal complexes: C:H.87, CMO.7 HEM.9: 19 residues within 4Å: Chain D: T.38, F.41, F.42, F.45, H.63, K.66, V.67, S.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.10 25 PLIP interactions: 24 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:V.67, D:F.71, D:F.71, D:L.88, D:L.91, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Water bridges: D:H.63, D:H.63 Salt bridges: D:H.63, D:K.66 pi-Stacking: D:H.92, D:H.92 Metal complexes: D:H.92, CMO.10

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

CMO.2: 5 residues within 4Å: Chain A: L.29, H.58, V.62, H.87 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CMO.5: 5 residues within 4Å: Chain B: F.42, H.63, V.67, H.92 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CMO.7: 5 residues within 4Å: Chain C: L.29, H.58, V.62, H.87 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) CMO.10: 5 residues within 4Å: Chain D: F.42, H.63, V.67, H.92 Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

2 x PEM: 2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID(Non-covalent)

PEM.3: 7 residues within 4Å: Chain A: A.57, K.60, K.61, D.64, A.65, L.83 Ligands: HEM.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.60, A:K.60, A:K.61, A:D.64, A:A.65 Hydrogen bonds: A:K.61 Water bridges: A:A.57, A:A.57, A:D.64, A:D.64 PEM.8: 7 residues within 4Å: Chain C: A.57, K.60, K.61, D.64, A.65, L.83 Ligands: HEM.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:K.60, C:K.60, C:K.61, C:D.64, C:A.65 Hydrogen bonds: C:K.61 Water bridges: C:A.57, C:A.57, C:D.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibayama, N. et al., Crystal Structure of Horse Carbonmonoxyhemoglobin-Bezafibrate Complex at 1.55A Resolution. A Novel Allosteric Binding Site in R-State Hemoglobin. J.BIOL.CHEM. (2002)

Release Date

2002-10-02

Peptides

Hemoglobin alpha chain: AC
Hemoglobin beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin alpha chain

Hemoglobin beta chain

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