SMTL ID : 2vee.2 (3 other biounits)

Structure of protoglobin from Methanosarcina acetivorans C2A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: L.70, Y.73, F.74, Y.85, V.89, R.92, F.93, W.96, Y.112, I.116, R.119, H.120, K.125, N.126, I.137, Y.141, L.142, F.145, I.146, I.149, T.178, V.182, W.185 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:Y.73, A:F.74, A:F.74, A:V.89, A:F.93, A:W.96, A:W.96, A:I.116, A:I.137, A:I.137, A:Y.141, A:L.142, A:F.145, A:F.145, A:F.145, A:I.149, A:T.178, A:V.182 Hydrogen bonds: A:Y.85, A:R.92, A:N.126 Water bridges: A:R.92, A:Q.127, A:D.129, A:D.129 Salt bridges: A:R.92, A:R.119 pi-Stacking: A:W.185 Metal complexes: A:H.120 HEM.2: 23 residues within 4Å: Chain B: L.70, Y.73, F.74, Y.85, V.89, R.92, F.93, W.96, Y.112, I.116, R.119, H.120, K.125, N.126, I.137, Y.141, L.142, F.145, I.146, I.149, T.178, V.182, W.185 30 PLIP interactions: 30 interactions with chain B, Hydrophobic interactions: B:Y.73, B:F.74, B:F.74, B:Y.85, B:V.89, B:F.93, B:W.96, B:W.96, B:I.116, B:I.137, B:I.137, B:Y.141, B:F.145, B:F.145, B:F.145, B:I.149, B:T.178, B:V.182 Hydrogen bonds: B:Y.85, B:Y.85, B:Y.112, B:N.126, B:T.128 Water bridges: B:R.92, B:R.92 Salt bridges: B:R.92, B:R.119 pi-Stacking: B:F.93, B:W.185 Metal complexes: B:H.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nardini, M. et al., Archaeal Protoglobin Structure Indicates New Ligand Diffusion Paths and Modulation of Haem-Reactivity. Embo Rep. (2008)

Release Date

2008-01-22

Peptides

PROTOGLOBIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

PROTOGLOBIN

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