SMTL ID : 8fdm.1

Human Hemoglobin in Complex with Nitrosomethane

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 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, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:F.43, A:K.61, A:V.62, 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:K.61 pi-Stacking: A:H.58, A:H.58 Metal complexes: A:H.87, H2O.1 HEM.6: 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, L.96, V.98, N.102, F.103, L.106, V.137, L.141 Ligands: NSM.7 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:F.42, B:V.67, B:F.71, B:F.71, B:L.88, B:L.91, B:L.96, B:V.98, B:V.98, B:N.102, B:F.103, B:L.106, B:V.137, B:L.141 Metal complexes: B:H.92 HEM.9: 17 residues within 4Å: Chain C: Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 20 PLIP interactions: 19 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:Y.42, C:Y.42, C:Y.42, C:F.43, C:F.43, C:K.61, C:V.62, C:L.83, C:L.86, C:L.91, C:V.93, C:V.93, C:F.98, C:L.136 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58, C:H.58 Metal complexes: C:H.87, H2O.5 HEM.13: 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, L.96, V.98, N.102, F.103, L.106, V.137, L.141 Ligands: NSM.14 18 PLIP interactions: 18 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:F.71, D:F.71, D:L.88, D:L.96, D:V.98, D:V.98, D:N.102, D:F.103, D:L.106, D:V.137, D:L.141 Metal complexes: D:H.92

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.20, Y.24, H.112 Chain B: K.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.112 GOL.3: 4 residues within 4Å: Chain A: F.43, P.44, F.46, L.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.46 GOL.5: 2 residues within 4Å: Chain A: K.99 Chain C: K.99 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.99, A:K.99, C:K.99 GOL.8: 6 residues within 4Å: Chain B: N.139, H.143, H.146 Chain D: N.139, H.143, H.146 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:N.139, B:H.143, B:H.146, D:N.139, D:N.139, D:H.143 GOL.10: 4 residues within 4Å: Chain C: H.20, Y.24, H.112 Chain D: K.120 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.20, C:Y.24, C:H.112

2 x MBN: TOLUENE(Non-covalent)

MBN.4: 5 residues within 4Å: Chain A: A.88, V.93, P.95, T.137 Chain D: W.37 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:A.88, A:P.95, A:T.137 pi-Stacking: D:W.37 MBN.11: 5 residues within 4Å: Chain B: W.37 Chain C: A.88, V.93, P.95, T.137 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C pi-Stacking: B:W.37 Hydrophobic interactions: C:A.88, C:P.95, C:T.137

2 x NSM: NITROSOMETHANE(Non-covalent)

NSM.7: 6 residues within 4Å: Chain B: L.28, F.42, H.63, V.67, L.106 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) NSM.14: 5 residues within 4Å: Chain D: F.42, H.63, V.67, L.106 Ligands: HEM.13 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 7 residues within 4Å: Chain C: A.26, E.30, H.50, G.51, S.52, V.55, K.56 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.30, C:G.51, C:S.52 Water bridges: C:E.27 Salt bridges: C:H.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Powell, S.M. et al., Crystal structural investigations of heme protein derivatives resulting from reactions of aryl- and alkylhydroxylamines with human hemoglobin. J.Inorg.Biochem. (2023)

Release Date

2023-07-12

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin subunit alpha

Hemoglobin subunit beta

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