SMTL ID : 4yu3.1

The crystal structure of mongoose (Helogale parvula) hemoglobin at pH 8.2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: T.39, Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: OXY.2 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:F.43, A:K.61, A:K.61, A:L.66, A:L.83, A:L.86, A:L.91, A:V.93, A:N.97, A:F.98, A:F.98, A:L.101, A:L.136 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58, A:H.58 Metal complexes: A:H.87 HEM.3: 16 residues within 4Å: Chain B: F.41, F.42, F.45, H.63, K.66, S.70, F.71, F.85, L.88, H.92, L.96, V.98, N.102, L.106, L.141 Ligands: OXY.4 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:F.71, B:F.85, B:L.88, B:L.96, B:V.98, B:N.102, B:L.141 pi-Stacking: B:H.63, B:H.63 Metal complexes: B:H.92 HEM.5: 19 residues within 4Å: Chain C: T.39, Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: OXY.6 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:Y.42, C:F.43, C:F.43, C:F.43, C:K.61, C:K.61, C:L.66, C:L.83, C:L.86, C:L.91, C:V.93, C:N.97, C:F.98, C:F.98, C:L.101, C:L.136 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58, C:H.58 Metal complexes: C:H.87 HEM.7: 16 residues within 4Å: Chain D: F.41, F.42, F.45, H.63, K.66, S.70, F.71, F.85, L.88, H.92, L.96, V.98, N.102, L.106, L.141 Ligands: OXY.8 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:F.41, D:F.41, D:F.42, D:F.42, D:F.42, D:F.71, D:F.85, D:L.88, D:L.96, D:V.98, D:N.102, D:L.141 pi-Stacking: D:H.63, D:H.63 Metal complexes: D:H.92

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 4 residues within 4Å: Chain A: F.43, H.58, V.62 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 OXY.4: 5 residues within 4Å: Chain B: F.42, H.63, V.67, H.92 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.63 OXY.6: 4 residues within 4Å: Chain C: F.43, H.58, V.62 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.58 OXY.8: 5 residues within 4Å: Chain D: F.42, H.63, V.67, H.92 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

Abubakkar, M.M. et al., The crystal structure of mongoose (Helogale parvula) hemoglobin at pH 8.2. To Be Published

Release Date

2015-09-23

Peptides

hemoglobin: AC
hemoglobin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

hemoglobin

hemoglobin

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