SMTL ID : 6bwu.1

Crystal structure of carboxyhemoglobin in complex with beta Cys93 modifying agent, TD3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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

CMO.1: 5 residues within 4Å: Chain A: L.29, F.43, H.58, V.62 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) CMO.3: 3 residues within 4Å: Chain B: F.42, H.63 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CMO.6: 5 residues within 4Å: Chain C: L.29, F.43, H.58, V.62 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CMO.8: 3 residues within 4Å: Chain D: F.42, H.63 Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

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

HEM.2: 20 residues within 4Å: Chain A: M.32, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.1 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.46, A:K.61, A:K.61, A:V.62, A:L.66, A:L.83, A:L.83, A:L.91, A:L.91, A:V.93, A:V.93, A:F.98, A:F.98, A:L.136 Water bridges: A:K.61, A:K.61, A:K.61 Salt bridges: A:H.45, A:H.58, A:K.61 Metal complexes: A:H.87 HEM.4: 19 residues within 4Å: Chain B: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, K.95, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.3 18 PLIP interactions: 17 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:L.88, B:L.91, B:L.96, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Salt bridges: B:K.95 Metal complexes: B:H.92, CMO.3 HEM.7: 20 residues within 4Å: Chain C: M.32, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.6 23 PLIP interactions: 23 interactions with chain C, Hydrophobic interactions: C:Y.42, C:F.43, C:F.46, C:K.61, C:K.61, C:V.62, C:L.66, C:L.83, C:L.83, C:L.91, C:L.91, C:V.93, C:V.93, C:F.98, C:F.98, C:L.136 Water bridges: C:H.58, C:K.61, C:K.61 Salt bridges: C:H.45, C:H.58, C:K.61 Metal complexes: C:H.87 HEM.9: 19 residues within 4Å: Chain D: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, K.95, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.8 18 PLIP interactions: 17 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:L.88, D:L.91, D:L.96, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Salt bridges: D:K.95 Metal complexes: D:H.92, CMO.8

2 x EBJ: 1H-1,2,3-triazole-5-thiol(Non-covalent)

EBJ.5: 5 residues within 4Å: Chain B: C.93, V.98, P.100, F.103, A.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.142 EBJ.10: 5 residues within 4Å: Chain D: C.93, V.98, P.100, F.103, A.142 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakagawa, A. et al., A Triazole Disulfide Compound Increases the Affinity of Hemoglobin for Oxygen and Reduces the Sickling of Human Sickle Cells. Mol. Pharm. (2018)

Release Date

2018-01-03

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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