SMTL ID : 3d1k.1

R/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-2-2-mer

Ligands

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

ACE.1: 4 residues within 4Å: Chain A: S.1, L.2, K.128 Chain C: L.135 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.135 ACE.5: 4 residues within 4Å: Chain A: L.135 Chain C: S.1, L.2, K.128 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.135

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.2: 4 residues within 4Å: Chain A: H.59, V.63, H.88 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) CMO.6: 4 residues within 4Å: Chain C: H.59, V.63, H.88 Ligands: HEM.7 No protein-ligand interaction detected (PLIP)

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

HEM.3: 21 residues within 4Å: Chain A: M.32, T.39, Y.42, F.43, H.45, W.46, H.59, K.62, V.63, I.67, L.84, Q.87, H.88, L.92, V.94, N.98, F.99, L.102, N.103, L.137 Ligands: CMO.2 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.39, A:Y.42, A:F.43, A:F.43, A:I.67, A:L.84, A:L.92, A:L.92, A:V.94, A:V.94, A:L.102, A:L.137 Hydrogen bonds: A:Q.87 Water bridges: A:K.62 Salt bridges: A:H.45, A:H.59, A:K.62, A:K.91 Metal complexes: A:H.88, CMO.2 HEM.4: 16 residues within 4Å: Chain B: T.38, Y.41, F.42, F.45, H.63, K.66, V.67, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:T.38, B:Y.41, B:Y.41, B:F.42, B:F.42, B:V.67, B:V.67, B:L.88, B:L.91, B:L.96, B:V.98, B:V.98, B:N.102, B:L.106, B:L.141 Water bridges: B:H.63 Salt bridges: B:H.63 Metal complexes: B:H.92, H2O.8 HEM.7: 21 residues within 4Å: Chain C: M.32, T.39, Y.42, F.43, H.45, W.46, H.59, K.62, V.63, I.67, L.84, Q.87, H.88, L.92, V.94, N.98, F.99, L.102, N.103, L.137 Ligands: CMO.6 21 PLIP interactions: 20 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:T.39, C:Y.42, C:F.43, C:F.43, C:I.67, C:L.84, C:L.92, C:L.92, C:V.94, C:V.94, C:L.102, C:L.137 Hydrogen bonds: C:Q.87 Water bridges: C:H.59, C:K.62 Salt bridges: C:H.45, C:H.59, C:K.62, C:K.91 Metal complexes: C:H.88, CMO.6 HEM.8: 16 residues within 4Å: Chain D: T.38, Y.41, F.42, F.45, H.63, K.66, V.67, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 18 PLIP interactions: 17 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:T.38, D:Y.41, D:Y.41, D:F.42, D:F.42, D:V.67, D:V.67, D:L.88, D:L.91, D:L.96, D:V.98, D:V.98, D:N.102, D:L.106, D:L.141 Salt bridges: D:H.63 Metal complexes: D:H.92, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vitagliano, L. et al., Spectroscopic and crystallographic characterization of a tetrameric hemoglobin oxidation reveals structural features of the functional intermediate relaxed/tense state. J.Am.Chem.Soc. (2008)

Release Date

2008-08-05

Peptides

Hemoglobin subunit alpha-1: AC
Hemoglobin subunit beta-1/2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin subunit alpha-1

Hemoglobin subunit beta-1/2

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