SMTL ID : 8wj1.1

cryo-EM structure of human haemoglobin in oxy form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.27 Å

Oligo State

hetero-3-3-mer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: Y.43, F.44, H.46, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Ligands: OXY.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.43, A:F.44, A:F.44, A:V.63, A:V.63, A:L.84, A:L.84, A:L.92, A:V.94, A:N.98, A:V.133, A:L.137 Salt bridges: A:H.46, A:K.62 pi-Stacking: A:H.59, A:H.59 Metal complexes: A:H.88 HEM.3: 17 residues within 4Å: Chain B: F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Ligands: OXY.4 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:F.42, B:F.42, B:F.43, B:F.43, B:F.43, B:V.68, B:V.68, B:A.71, B:L.89, B:L.92, B:L.97, B:L.97, B:V.99, B:N.103, B:L.107, B:L.142 Salt bridges: B:H.64, B:K.67 pi-Stacking: B:H.64 Metal complexes: B:H.93 HEM.5: 39 residues within 4Å: Chain C: Y.43, F.44, H.46, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Chain E: Y.43, F.44, H.46, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Ligands: OXY.6, HEM.9, OXY.10 23 PLIP interactions: 17 interactions with chain C, 6 interactions with chain E, Hydrophobic interactions: C:Y.43, C:F.44, C:F.44, C:V.63, C:V.63, C:L.84, C:L.84, C:L.92, C:V.94, C:N.98, C:V.133, C:L.137, E:K.62, E:H.88 Water bridges: C:H.46, C:H.46 Salt bridges: C:H.46, C:K.62, E:H.46, E:K.62 Metal complexes: C:H.88 pi-Stacking: E:H.59, E:H.59 HEM.7: 35 residues within 4Å: Chain D: F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Chain F: F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Ligands: OXY.8, HEM.11, OXY.12 24 PLIP interactions: 20 interactions with chain D, 4 interactions with chain F, Hydrophobic interactions: D:F.42, D:F.42, D:F.43, D:F.43, D:F.43, D:K.67, D:V.68, D:V.68, D:A.71, D:L.89, D:L.92, D:L.97, D:L.97, D:V.99, D:L.107, D:L.142, F:N.103 Salt bridges: D:H.64, D:K.67, F:H.64, F:K.67 pi-Cation interactions: D:H.64, F:H.64 Metal complexes: D:H.93 HEM.9: 39 residues within 4Å: Chain C: Y.43, F.44, H.46, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Chain E: Y.43, F.44, H.46, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Ligands: HEM.5, OXY.6, OXY.10 23 PLIP interactions: 17 interactions with chain C, 6 interactions with chain E, Hydrophobic interactions: C:Y.43, C:F.44, C:F.44, C:V.63, C:V.63, C:L.84, C:L.84, C:L.92, C:V.94, C:N.98, C:V.133, C:L.137, E:K.62, E:H.88 Water bridges: C:H.46, C:H.46 Salt bridges: C:H.46, C:K.62, E:H.46, E:K.62 Metal complexes: C:H.88 pi-Stacking: E:H.59, E:H.59 HEM.11: 35 residues within 4Å: Chain D: F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Chain F: F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Ligands: HEM.7, OXY.8, OXY.12 24 PLIP interactions: 20 interactions with chain D, 4 interactions with chain F, Hydrophobic interactions: D:F.42, D:F.42, D:F.43, D:F.43, D:F.43, D:K.67, D:V.68, D:V.68, D:A.71, D:L.89, D:L.92, D:L.97, D:L.97, D:V.99, D:L.107, D:L.142, F:N.103 Salt bridges: D:H.64, D:K.67, F:H.64, F:K.67 pi-Cation interactions: D:H.64, F:H.64 Metal complexes: D:H.93

6 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 4 residues within 4Å: Chain A: L.30, H.59, V.63 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.59 OXY.4: 3 residues within 4Å: Chain B: H.64, V.68 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.64 OXY.6: 9 residues within 4Å: Chain C: L.30, H.59, V.63 Chain E: L.30, H.59, V.63 Ligands: HEM.5, HEM.9, OXY.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.59, C:H.59 OXY.8: 7 residues within 4Å: Chain D: H.64, V.68 Chain F: H.64, V.68 Ligands: HEM.7, HEM.11, OXY.12 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:H.64, D:H.64, D:H.64, D:H.93, F:H.64 OXY.10: 9 residues within 4Å: Chain C: L.30, H.59, V.63 Chain E: L.30, H.59, V.63 Ligands: HEM.5, OXY.6, HEM.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.59 OXY.12: 7 residues within 4Å: Chain D: H.64, V.68 Chain F: H.64, V.68 Ligands: HEM.7, OXY.8, HEM.11 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:H.64, D:H.93, F:H.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takahashi, K. et al., The unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM. Nat Commun (2024)

Release Date

2024-08-14

Peptides

Hemoglobin subunit alpha: ACE
Hemoglobin subunit beta: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemoglobin subunit alpha

Hemoglobin subunit beta

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