SMTL ID : 1v75.1

Crystal structure of hemoglobin D from the Aldabra giant tortoise (Geochelone gigantea) at 2.0 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: M.32, Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, H.87, L.91, V.93, N.97, F.98, L.101, L.136 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Y.42, A:Y.42, A:F.43, A:K.61, A:A.65, A:L.66, A:L.83, A:L.91, A:L.91, A:V.93, A:N.97, A:L.136 Water bridges: A:H.57, A:H.58 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58, A:H.87, A:H.87 Metal complexes: A:H.87, H2O.10 HEM.2: 18 residues within 4Å: Chain B: L.31, T.38, F.41, F.42, F.45, H.63, K.66, V.67, S.70, F.71, L.88, H.92, L.96, V.98, N.102, F.103, L.106, L.141 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:L.31, B:T.38, B:F.41, B:F.41, B:F.42, B:V.67, B:L.88, B:L.96, B:V.98, B:N.102, B:F.103, B:F.103, B:L.106, B:L.141 Water bridges: B:H.63 Salt bridges: B:K.59, B:K.66 pi-Stacking: B:H.63, B:H.63, B:H.92 Metal complexes: B:H.92, H2O.16 HEM.3: 17 residues within 4Å: Chain C: M.32, Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, H.87, L.91, V.93, N.97, F.98, L.101, L.136 20 PLIP interactions: 19 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:K.61, C:A.65, C:L.66, C:L.83, C:L.91, C:L.91, C:V.93, C:N.97, C:L.136 Water bridges: C:H.58 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58, C:H.87, C:H.87 Metal complexes: C:H.87, H2O.26 HEM.4: 18 residues within 4Å: Chain D: L.31, T.38, F.41, F.42, F.45, H.63, K.66, V.67, S.70, F.71, L.88, H.92, L.96, V.98, N.102, F.103, L.106, L.141 22 PLIP interactions: 21 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:L.31, D:T.38, D:F.41, D:F.41, D:F.42, D:V.67, D:L.88, D:L.96, D:V.98, D:N.102, D:F.103, D:F.103, D:L.106, D:L.141 Water bridges: D:H.63 Salt bridges: D:K.59, D:K.66 pi-Stacking: D:H.63, D:H.63, D:H.92 Metal complexes: D:H.92, H2O.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuwada, T. et al., Crystallization and preliminary X-ray diffraction study of hemoglobin D from the Aldabra giant tortoise, Geochelone gigantea. Protein Pept.Lett. (2003)

Release Date

2003-12-30

Peptides

Hemoglobin D alpha chain: AC
Hemoglobin A and D beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin D alpha chain

Hemoglobin A and D beta chain

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