SMTL ID : 3vrf.1

The crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy forms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 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: Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, V.132, L.136 Ligands: CMO.2 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:F.43, A:V.62, A:V.62, A:A.65, A:L.83, A:L.91, A:V.93, A:F.98, A:V.132, A:L.136 Salt bridges: A:H.45, A:H.58, A:K.61 Metal complexes: A:H.87, CMO.2 HEM.3: 20 residues within 4Å: Chain B: T.38, F.41, F.42, H.44, F.45, H.63, K.66, V.67, S.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.4 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:F.45, B:V.67, B:V.67, B:F.71, B:F.71, B:L.88, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Salt bridges: B:H.44, B:H.63 Metal complexes: B:H.92, CMO.4 HEM.5: 19 residues within 4Å: Chain C: Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, V.132, L.136 Ligands: CMO.6 19 PLIP interactions: 18 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.42, C:Y.42, C:Y.42, C:F.43, C:F.43, C:V.62, C:V.62, C:A.65, C:L.83, C:L.91, C:V.93, C:F.98, C:V.132, C:L.136 Salt bridges: C:H.45, C:H.58, C:K.61 Metal complexes: C:H.87, CMO.6 HEM.7: 20 residues within 4Å: Chain D: T.38, F.41, F.42, H.44, F.45, H.63, K.66, V.67, S.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.8 22 PLIP interactions: 21 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:F.42, D:F.45, D:V.67, D:V.67, D:F.71, D:F.71, D:L.88, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Salt bridges: D:H.44, D:H.63 Metal complexes: D:H.92, CMO.8

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

CMO.2: 6 residues within 4Å: Chain A: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CMO.4: 6 residues within 4Å: Chain B: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) CMO.6: 6 residues within 4Å: Chain C: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) CMO.8: 6 residues within 4Å: Chain D: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noguchi, H. et al., Structures of haemoglobin from woolly mammoth in liganded and unliganded states. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-11-07

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta/delta hybrid: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin subunit alpha

Hemoglobin subunit beta/delta hybrid

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