SMTL ID : 4odc.1

Crystal structure of Trematomus bernacchii hemoglobin in a partially cyanided state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

hetero-2-2-mer

Ligands

4 x CYN: CYANIDE ION(Non-covalent)

CYN.1: 5 residues within 4Å: Chain A: L.30, F.44, H.60, V.64 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) CYN.3: 3 residues within 4Å: Chain B: H.63, V.67 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CYN.6: 5 residues within 4Å: Chain C: L.30, F.44, H.60, V.64 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CYN.8: 3 residues within 4Å: Chain D: H.63, V.67 Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

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

HEM.2: 21 residues within 4Å: Chain A: M.33, T.40, Y.43, F.44, H.46, W.47, H.60, K.63, V.64, I.68, L.85, Q.88, H.89, L.93, V.95, N.99, F.100, L.103, N.104, L.138 Ligands: CYN.1 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:T.40, A:Y.43, A:F.44, A:I.68, A:L.85, A:L.93, A:L.93, A:V.95, A:V.95, A:L.103, A:L.138 Hydrogen bonds: A:W.47, A:Q.88 Water bridges: A:H.60, A:K.63 Salt bridges: A:H.46, A:H.60, A:K.63, A:K.92 pi-Stacking: A:H.60 Metal complexes: A:H.89, H2O.1 HEM.4: 15 residues within 4Å: Chain B: H.41, F.42, H.63, K.66, V.67, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CYN.3 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:F.42, B:F.42, B:F.42, B:K.66, B:V.67, B:L.88, B:L.91, B:L.96, B:V.98, B:L.106, B:L.141 Salt bridges: B:H.63, B:K.66, B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.7: 21 residues within 4Å: Chain C: M.33, T.40, Y.43, F.44, H.46, W.47, H.60, K.63, V.64, I.68, L.85, Q.88, H.89, L.93, V.95, N.99, F.100, L.103, N.104, L.138 Ligands: CYN.6 21 PLIP interactions: 20 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:T.40, C:Y.43, C:F.44, C:I.68, C:L.85, C:L.93, C:L.93, C:V.95, C:V.95, C:L.103, C:L.138 Hydrogen bonds: C:W.47, C:Q.88 Water bridges: C:K.63 Salt bridges: C:H.46, C:H.60, C:K.63, C:K.92 pi-Stacking: C:H.60 Metal complexes: C:H.89, H2O.16 HEM.9: 15 residues within 4Å: Chain D: H.41, F.42, H.63, K.66, V.67, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CYN.8 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:F.42, D:F.42, D:F.42, D:K.66, D:V.67, D:L.88, D:L.91, D:L.96, D:V.98, D:L.106, D:L.141 Salt bridges: D:H.63, D:K.66, D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain B: H.146 Chain D: V.1, M.78, D.79, N.80, I.81, A.82, V.136 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:V.1, D:M.78, D:I.81, D:A.82 Water bridges: D:V.1, B:H.146, B:H.146 GOL.10: 8 residues within 4Å: Chain B: V.1, M.78, D.79, N.80, I.81, A.82, V.136 Chain D: H.146 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:V.1, B:V.1, B:M.78, B:I.81, B:A.82 Water bridges: B:D.79, D:H.146

Links

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Citation

Mazzarella, L. et al., Structural modifications induced by the switch from an endogenous bis-histidyl to an exogenous cyanomet hexa-coordination in a tetrameric haemoglobin. RSC ADV (2014)

Release Date

2014-12-24

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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