SMTL ID : 9cqs.1

Human OxyHb (C1 symmetry) obtained using the SPT Labtech chameleon In the presence of 5 mM sodium dithionite under Al's oil

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: Y.41, F.42, H.44, F.45, H.57, K.60, V.61, A.64, L.65, L.82, L.85, H.86, L.90, V.92, N.96, F.97, L.100, V.131, L.135 Ligands: OXY.2 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.41, A:F.42, A:F.42, A:K.60, A:K.60, A:V.61, A:V.61, A:L.65, A:L.82, A:L.85, A:L.90, A:V.92, A:F.97, A:L.100, A:V.131, A:L.135 Salt bridges: A:H.44 pi-Stacking: A:H.57 Metal complexes: A:H.86 HEM.3: 19 residues within 4Å: Chain B: T.37, F.40, F.41, H.62, K.65, V.66, A.69, F.70, L.87, L.90, H.91, K.94, L.95, V.97, N.101, F.102, L.105, L.140 Ligands: OXY.4 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:T.37, B:F.40, B:F.40, B:F.41, B:F.41, B:F.41, B:V.66, B:V.66, B:F.70, B:L.87, B:L.95, B:L.95, B:V.97, B:N.101, B:L.105, B:L.140 Salt bridges: B:K.94 pi-Stacking: B:H.62 Metal complexes: B:H.91 HEM.5: 18 residues within 4Å: Chain C: Y.41, F.42, F.45, H.57, K.60, V.61, A.64, L.82, L.85, H.86, L.90, V.92, N.96, F.97, L.100, V.131, L.135 Ligands: OXY.6 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.41, C:Y.41, C:F.42, C:F.42, C:K.60, C:V.61, C:V.61, C:A.64, C:L.90, C:V.92, C:F.97, C:L.100, C:V.131, C:L.135 Water bridges: C:K.60 Salt bridges: C:H.44 pi-Stacking: C:H.57 Metal complexes: C:H.86 HEM.7: 18 residues within 4Å: Chain D: T.37, F.40, F.41, H.62, K.65, V.66, A.69, F.70, L.87, L.90, H.91, L.95, V.97, N.101, F.102, L.105, L.140 Ligands: OXY.8 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:T.37, D:F.40, D:F.41, D:F.41, D:F.41, D:V.66, D:V.66, D:L.87, D:L.90, D:L.90, D:L.95, D:V.97, D:N.101, D:F.102, D:F.102, D:L.105, D:L.140 pi-Stacking: D:H.62 Metal complexes: D:H.91

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 4 residues within 4Å: Chain A: H.57, V.61, H.86 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.57 OXY.4: 5 residues within 4Å: Chain B: L.27, H.62, V.66, H.91 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.62 OXY.6: 4 residues within 4Å: Chain C: L.28, H.57, V.61 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.57 OXY.8: 4 residues within 4Å: Chain D: H.62, V.66, H.91 Ligands: HEM.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, B.D. et al., Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using blot-free vitrification. Nat Commun (2025)

Release Date

2025-04-30

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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