SMTL ID : 3bj2.1

met-Perch Hemoglobin at pH 6.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 16 residues within 4Å: Chain A: M.32, T.39, Y.42, F.43, H.59, T.62, I.63, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:T.62, A:I.63, A:I.63, A:L.84, A:L.87, A:L.92, A:V.94, A:V.94, A:L.102, A:L.137 Hydrogen bonds: A:W.46 Salt bridges: A:H.45, A:H.59 pi-Stacking: A:H.59 pi-Cation interactions: A:H.88 Metal complexes: A:H.88, H2O.1 HEM.3: 17 residues within 4Å: Chain B: Y.41, F.42, F.45, K.62, H.63, T.66, I.67, L.71, R.73, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.141 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.41, B:Y.41, B:F.42, B:F.42, B:F.42, B:F.45, B:T.66, B:I.67, B:L.71, B:L.88, B:L.91, B:L.96, B:V.98, B:F.103, B:L.141 Salt bridges: B:K.62, B:H.63 pi-Stacking: B:H.63, B:H.63 Metal complexes: B:H.92, H2O.2 HEM.4: 17 residues within 4Å: Chain C: T.39, Y.42, F.43, H.45, H.59, T.62, I.63, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 20 PLIP interactions: 19 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:T.39, C:Y.42, C:Y.42, C:F.43, C:F.43, C:T.62, C:I.63, C:L.84, C:L.87, C:L.92, C:V.94, C:V.94, C:F.99, C:F.99, C:L.102, C:L.137 Salt bridges: C:H.45, C:H.59 Metal complexes: C:H.88, H2O.5 HEM.6: 15 residues within 4Å: Chain D: Y.41, F.42, F.45, H.63, T.66, L.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 16 PLIP interactions: 15 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:Y.41, D:Y.41, D:F.42, D:F.42, D:F.42, D:F.45, D:L.88, D:L.91, D:L.96, D:V.98, D:F.103, D:L.141 Water bridges: D:H.63 pi-Stacking: D:H.63 Metal complexes: D:H.92, H2O.8

2 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.2: 5 residues within 4Å: Chain A: S.1, L.2, K.128, R.135 Chain C: E.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.1, A:R.135 ACE.5: 4 residues within 4Å: Chain A: E.139 Chain C: S.1, L.2, K.128 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aranda, R. et al., Structural analysis of fish versus mammalian hemoglobins: Effect of the heme pocket environment on autooxidation and hemin loss. Proteins (2008)

Release Date

2008-09-02

Peptides

hemoglobin alpha: AC
hemoglobin beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

hemoglobin alpha

hemoglobin beta

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