SMTL ID : 8wj2.1

cryo-EM structure of human haemoglobin in deoxy form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.35 Å

Oligo State

hetero-3-3-mer

Ligands

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

HEM.1: 17 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, L.137 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:Y.43, A:F.44, A:F.44, A:F.44, A:V.63, A:V.63, A:A.66, A:L.84, A:L.87, A:L.92, A:L.92, A:V.94, A:N.98, A:F.99, A:F.99, A:L.102, A:L.137 Salt bridges: A:H.46 pi-Stacking: A:H.59, A:H.59 Metal complexes: A:H.88 HEM.2: 16 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 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.42, B:F.42, B:F.43, B:F.43, B:F.43, B:K.67, B:V.68, B:V.68, B:A.71, B:F.72, B:L.89, B:L.92, 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.3: 35 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, 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, L.137 Ligands: HEM.5 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:Y.43, C:F.44, C:F.44, C:F.44, C:H.59, C:K.62, C:V.63, C:V.63, C:A.66, C:L.84, C:L.87, C:L.92, C:L.92, C:V.94, C:N.98, C:N.98, C:F.99, C:F.99, C:L.102, C:L.137 Salt bridges: C:H.46, E:H.46 pi-Cation interactions: C:H.59, C:H.59, E:H.59, E:H.59 Metal complexes: C:H.88 HEM.4: 33 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.6 26 PLIP interactions: 22 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:F.72, D:L.89, D:L.92, D:H.93, D:L.97, D:V.99, D:N.103, D:L.107, D:L.142, F:H.64 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.5: 35 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, 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, L.137 Ligands: HEM.3 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:Y.43, C:F.44, C:F.44, C:F.44, C:H.59, C:K.62, C:V.63, C:V.63, C:A.66, C:L.84, C:L.87, C:L.92, C:L.92, C:V.94, C:N.98, C:N.98, C:F.99, C:F.99, C:L.102, C:L.137 Salt bridges: C:H.46, E:H.46 pi-Cation interactions: C:H.59, C:H.59, E:H.59, E:H.59 Metal complexes: C:H.88 HEM.6: 33 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.4 26 PLIP interactions: 22 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:F.72, D:L.89, D:L.92, D:H.93, D:L.97, D:V.99, D:N.103, D:L.107, D:L.142, F:H.64 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

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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