SMTL ID : 8fdn.1

Human Hemoglobin with N-tertbutylhydroxylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: V.96, K.99 Chain B: E.101, R.104 Chain C: V.96, K.99 Chain D: E.101, R.104 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:E.101, B:R.104, C:K.99, A:K.99 GOL.3: 3 residues within 4Å: Chain A: Y.24, H.112 Chain B: K.120 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.24, A:H.112, A:H.112, B:K.120 GOL.8: 5 residues within 4Å: Chain C: H.20, Y.24, H.112, L.113 Chain D: K.120 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.24, C:H.112 GOL.9: 6 residues within 4Å: Chain B: P.36 Chain C: A.88, H.89, R.92, K.139, Y.140 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.92, C:K.139

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

HEM.2: 23 residues within 4Å: Chain A: M.32, T.39, 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.105, L.129, V.132, L.136 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:K.61, A:V.62, A:V.62, A:L.66, A:L.83, A:L.86, A:L.91, A:V.93, A:F.98, A:F.98, 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.4: 17 residues within 4Å: Chain B: F.41, F.42, S.44, F.45, H.63, K.66, V.67, A.70, L.88, L.91, H.92, K.95, L.96, F.103, L.106, L.141 Ligands: XQZ.5 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:F.42, B:K.66, B:K.66, B:A.70, B:L.88, B:L.91, B:K.95 Salt bridges: B:H.63, B:K.66, B:K.66 Metal complexes: B:H.92 HEM.6: 23 residues within 4Å: Chain C: M.32, T.39, 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.105, L.129, V.132, L.136 22 PLIP interactions: 21 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:F.43, C:K.61, C:V.62, C:V.62, C:L.66, C:L.83, C:L.86, C:L.91, C:L.91, C:V.93, C:F.98, C:L.136 Water bridges: C:H.58 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58, C:H.58 Metal complexes: C:H.87, H2O.3 HEM.11: 17 residues within 4Å: Chain D: F.41, F.42, S.44, F.45, K.59, H.63, K.66, V.67, A.70, L.88, L.91, H.92, K.95, L.96, F.103, L.106 Ligands: XQZ.12 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:F.42, D:K.66, D:V.67, D:A.70, D:L.91, D:K.95 Salt bridges: D:K.59, D:H.63, D:K.66, D:K.66 Metal complexes: D:H.63, D:H.92

4 x XQZ: N-T-Butylhydroxylamine(Non-covalent)

XQZ.5: 11 residues within 4Å: Chain B: L.31, T.38, F.41, F.42, K.95, L.96, V.98, N.102, F.103, L.106 Ligands: HEM.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.41, B:N.102, B:F.103, B:F.103 XQZ.7: 1 residues within 4Å: Chain C: H.50 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.50 XQZ.10: 3 residues within 4Å: Chain C: A.5, T.8, N.9 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.8 XQZ.12: 11 residues within 4Å: Chain D: L.31, T.38, F.41, F.42, K.95, L.96, V.98, N.102, F.103, L.106 Ligands: HEM.11 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.98, D:V.98, D:N.102, D:F.103, D:F.103

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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