SMTL ID : 5c6e.1

Joint X-ray/neutron structure of equine cyanomet hemoglobin in R state

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: M.32, T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.105, L.129, V.132, S.133, L.136 Ligands: CYN.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:F.43, A:K.61, A:A.65, A:L.83, A:L.91, A:V.93, A:F.98, A:F.98, A:L.136 Water bridges: A:H.45, A:K.61 Salt bridges: A:H.45, A:K.61, A:K.61 Metal complexes: A:H.87 HEM.3: 23 residues within 4Å: Chain B: L.31, T.38, F.41, F.42, S.44, F.45, H.63, K.66, V.67, S.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, V.137, L.141 Ligands: CYN.4 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:F.41, B:F.42, B:F.42, B:F.42, B:V.67, B:S.70, B:F.71, B:L.88, B:L.96, B:V.98, B:N.102, B:L.141 Water bridges: B:H.63, B:K.66 Salt bridges: B:H.63, B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.5: 25 residues within 4Å: Chain C: M.32, T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.105, L.129, V.132, S.133, L.136 Ligands: CYN.6 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:K.61, C:A.65, C:L.83, C:L.91, C:V.93, C:F.98, C:F.98, C:L.136 Water bridges: C:H.45, C:K.61 Salt bridges: C:H.45, C:K.61, C:K.61 Metal complexes: C:H.87 HEM.7: 23 residues within 4Å: Chain D: L.31, T.38, F.41, F.42, S.44, F.45, H.63, K.66, V.67, S.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, V.137, L.141 Ligands: CYN.8 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:F.41, D:F.42, D:F.42, D:F.42, D:V.67, D:S.70, D:F.71, D:L.88, D:L.96, D:V.98, D:N.102, D:L.141 Water bridges: D:H.63, D:K.66 Salt bridges: D:H.63, D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

4 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 6 residues within 4Å: Chain A: L.29, F.43, H.58, V.62, L.101 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 CYN.4: 5 residues within 4Å: Chain B: L.28, F.42, H.63, V.67 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.63 CYN.6: 6 residues within 4Å: Chain C: L.29, F.43, H.58, V.62, L.101 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.58 CYN.8: 5 residues within 4Å: Chain D: L.28, F.42, H.63, V.67 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dajnowicz, S. et al., Visualizing the Bohr effect in hemoglobin: neutron structure of equine cyanomethemoglobin in the R state and comparison with human deoxyhemoglobin in the T state. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-06-22

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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