SMTL ID : 8wiz.1

cryo-EM structure of alligator haemoglobin in deoxy form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: Y.43, F.44, H.46, F.47, H.59, K.62, V.63, L.67, R.83, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.43, A:F.44, A:F.44, A:V.63, A:L.84, A:L.87, A:L.92, A:L.92, A:V.94, A:V.94, A:N.98, A:F.99, A:L.102, A:L.137 Salt bridges: A:H.46, A:R.83 pi-Stacking: A:H.59 Metal complexes: A:H.88 HEM.2: 16 residues within 4Å: Chain B: Y.41, F.42, H.44, H.63, K.66, V.67, S.70, F.71, L.88, H.92, F.96, V.98, N.102, F.103, L.106, L.141 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:Y.41, B:F.42, B:K.66, B:V.67, B:V.67, B:F.71, B:L.88, B:F.96, B:F.96, B:F.96, B:F.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Salt bridges: B:H.44 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.4: 18 residues within 4Å: Chain C: Y.43, F.44, H.46, F.47, H.59, K.62, V.63, L.67, R.83, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.43, C:F.44, C:F.44, C:V.63, C:L.84, C:L.87, C:L.92, C:L.92, C:V.94, C:V.94, C:N.98, C:F.99, C:L.102, C:L.137 Salt bridges: C:H.46, C:R.83 pi-Stacking: C:H.59 Metal complexes: C:H.88 HEM.5: 16 residues within 4Å: Chain D: Y.41, F.42, H.44, H.63, K.66, V.67, S.70, F.71, L.88, H.92, F.96, V.98, N.102, F.103, L.106, L.141 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:Y.41, D:F.42, D:K.66, D:V.67, D:V.67, D:F.71, D:L.88, D:F.96, D:F.96, D:F.96, D:F.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Salt bridges: D:H.44 pi-Stacking: D:H.63 Metal complexes: D:H.92

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.3: 9 residues within 4Å: Chain B: W.37, K.38, R.40, Y.41, D.99, N.102 Chain C: Y.43, R.93, D.95 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.38, B:K.38, B:R.40, B:R.40, B:N.102 BCT.6: 9 residues within 4Å: Chain A: Y.43, R.93, D.95 Chain D: W.37, K.38, R.40, Y.41, D.99, N.102 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.38, D:K.38, D:R.40, D:R.40, D:N.102

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: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin subunit alpha

Hemoglobin subunit beta

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