SMTL ID : 5lfg.2 (1 other biounit)

X-ray structure of a new fully ligated carbomonoxy form of Trematomus newnesi hemoglobin (Hb1TnCO).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-oligomer

Ligands

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

CMO.1: 4 residues within 4Å: Chain A: H.60, V.64, H.89 Ligands: HEM.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.60, A:V.64 CMO.4: 4 residues within 4Å: Chain B: H.63, V.67, H.92 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) CMO.5: 4 residues within 4Å: Chain C: H.60, V.64, H.89 Ligands: HEM.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.60, C:V.64 CMO.8: 4 residues within 4Å: Chain D: H.63, V.67, H.92 Ligands: HEM.7 No protein-ligand interaction detected (PLIP)

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

HEM.2: 20 residues within 4Å: Chain A: Y.43, F.44, H.46, W.47, H.60, K.63, V.64, G.67, I.68, L.85, Q.88, H.89, K.92, L.93, V.95, N.99, F.100, L.103, L.138 Ligands: CMO.1 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.43, A:Y.43, A:F.44, A:F.44, A:K.63, A:L.85, A:L.93, A:L.93, A:V.95, A:V.95, A:N.99, A:F.100, A:L.103, A:L.138 Salt bridges: A:H.46, A:K.63, A:K.92, A:K.92 Metal complexes: A:H.89, CMO.1 HEM.3: 18 residues within 4Å: Chain B: T.38, Y.41, F.42, F.45, H.63, K.66, V.67, R.73, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.4 18 PLIP interactions: 17 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.38, B:Y.41, B:F.42, B:F.42, B:F.45, B:L.88, B:L.91, B:L.96, B:V.98, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Salt bridges: B:H.63, B:K.66 Metal complexes: B:H.92, CMO.4 HEM.6: 20 residues within 4Å: Chain C: Y.43, F.44, H.46, W.47, H.60, K.63, V.64, G.67, I.68, L.85, Q.88, H.89, K.92, L.93, V.95, N.99, F.100, L.103, L.138 Ligands: CMO.5 20 PLIP interactions: 19 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.43, C:Y.43, C:F.44, C:F.44, C:K.63, C:L.85, C:L.93, C:L.93, C:V.95, C:V.95, C:N.99, C:F.100, C:L.103, C:L.138 Salt bridges: C:H.46, C:K.63, C:K.92, C:K.92 Metal complexes: C:H.89, CMO.5 HEM.7: 18 residues within 4Å: Chain D: T.38, Y.41, F.42, F.45, H.63, K.66, V.67, R.73, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.8 18 PLIP interactions: 17 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.38, D:Y.41, D:F.42, D:F.42, D:F.45, D:L.88, D:L.91, D:L.96, D:V.98, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Salt bridges: D:H.63, D:K.66 Metal complexes: D:H.92, CMO.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vitagliano, L. et al., Fine Sampling of the RT Quaternary-Structure Transition of a Tetrameric Hemoglobin. Chemistry (2017)

Release Date

2017-08-09

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
C

B
D

D
D

Hemoglobin subunit alpha-1

Hemoglobin subunit beta-1/2

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