SMTL ID : 9cqn.1

Human OxyHb (C2 symmetry) obtained using the SPT Labtech chameleon In the presence of 25 uM 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 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.41, A:F.42, A:K.60, A:V.61, A:V.61, A:L.65, A:L.82, A:L.90, A:V.92, A:F.97, A:V.131, A:L.135 Water bridges: A:H.57 Salt bridges: A:H.44, A:K.60 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 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:T.37, B:F.40, B:F.40, B:F.41, B:V.66, B:V.66, B:L.87, B:L.95, B:L.95, B:V.97, B:F.102, B:L.105, B:L.140 Salt bridges: B:K.65, 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, H.44, 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, L.135 Ligands: OXY.6 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.41, C:F.42, C:F.42, C:K.60, C:V.61, C:V.61, C:L.82, C:L.90, C:L.90, C:V.92, C:N.96, C:F.97, C:L.135 Water bridges: C:H.57 Salt bridges: C:H.44, C:K.60 pi-Stacking: C:H.57 Metal complexes: C:H.86 HEM.7: 19 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, K.94, L.95, V.97, N.101, F.102, L.105, L.140 Ligands: OXY.8 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:T.37, D:F.40, D:F.40, D:F.41, D:F.41, D:F.41, D:V.66, D:V.66, D:L.87, D:L.95, D:L.95, D:V.97, D:N.101, D:L.105, D:L.140 Salt bridges: D:K.94 pi-Stacking: D:H.62 Metal complexes: D:H.91

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 3 residues within 4Å: Chain A: H.57, V.61 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.57 OXY.4: 5 residues within 4Å: Chain B: F.41, H.62, V.66, H.91 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.62 OXY.6: 6 residues within 4Å: Chain C: L.28, F.42, H.57, V.61, L.100 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) OXY.8: 5 residues within 4Å: Chain D: F.41, H.62, V.66, H.91 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.62

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

Related Entries With Identical Sequence