SMTL ID : 4m4a.1

Human Hemoglobin Nitromethane Modified

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: Y.42, F.43, H.45, 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: NSM.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:F.46, A:L.83, A:L.83, A:L.86, A:L.91, A:V.93, A:F.98, A:L.101, A:L.136 Salt bridges: A:H.45, A:H.58, A:K.61 Metal complexes: A:H.87 HEM.5: 18 residues within 4Å: Chain B: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, H.92, L.96, V.98, N.102, F.103, L.106, V.137, L.141 Ligands: NSM.6 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:V.67, B:A.70, B:F.71, B:F.71, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:V.137, B:L.141 Water bridges: B:K.66, B:K.66 Salt bridges: B:K.66 Metal complexes: B:H.92 HEM.8: 17 residues within 4Å: Chain C: Y.42, F.43, H.45, 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: NSM.9 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:Y.42, C:F.43, C:F.46, C:L.83, C:L.83, C:L.86, C:L.91, C:V.93, C:F.98, C:L.101, C:L.136 Salt bridges: C:H.45, C:H.58, C:K.61 Metal complexes: C:H.87 HEM.12: 18 residues within 4Å: Chain D: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, H.92, L.96, V.98, N.102, F.103, L.106, V.137, L.141 Ligands: NSM.13 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:A.70, D:F.71, D:F.71, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:V.137, D:L.141 Water bridges: D:K.66, D:K.66 Salt bridges: D:K.66 Metal complexes: D:H.92

4 x NSM: NITROSOMETHANE(Non-covalent)

NSM.2: 6 residues within 4Å: Chain A: L.29, F.43, H.58, V.62, L.101 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) NSM.6: 5 residues within 4Å: Chain B: F.42, H.63, V.67, L.106 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) NSM.9: 6 residues within 4Å: Chain C: L.29, F.43, H.58, V.62, L.101 Ligands: HEM.8 No protein-ligand interaction detected (PLIP) NSM.13: 5 residues within 4Å: Chain D: F.42, H.63, V.67, L.106 Ligands: HEM.12 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: A.26, E.27, E.30, S.49, H.50, G.51, S.52, V.55, K.56 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.26, A:H.50, A:G.51, A:S.52, A:K.56 GOL.4: 6 residues within 4Å: Chain A: F.43, P.44, H.45, F.46, D.47, L.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.43, A:P.44 Water bridges: A:L.48 GOL.7: 7 residues within 4Å: Chain B: N.139, H.143, H.146 Chain D: N.139, H.143, H.146 Ligands: GOL.14 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:N.139, B:H.146, D:H.146 Water bridges: D:K.82, D:H.143 GOL.10: 9 residues within 4Å: Chain C: A.26, E.27, E.30, S.49, H.50, G.51, S.52, V.55, K.56 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.26, C:H.50, C:G.51, C:S.52, C:K.56 GOL.11: 6 residues within 4Å: Chain C: F.43, P.44, H.45, F.46, D.47, L.48 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.43, C:P.44, C:D.47 Water bridges: C:L.48 GOL.14: 7 residues within 4Å: Chain B: N.139, H.143, H.146 Chain D: N.139, H.143, H.146 Ligands: GOL.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.146, D:H.146 Water bridges: B:K.82, B:H.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yi, J. et al., Degradation of human hemoglobin by organic C-nitroso compounds. Chem.Commun.(Camb.) (2013)

Release Date

2014-07-16

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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