SMTL ID : 3zol.1

M.acetivorans protoglobin F93Y mutant in complex with cyanide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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, Y.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, V.182, W.185 Ligands: CYN.2 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:Y.73, A:F.74, A:F.74, A:F.74, A:Y.85, A:V.89, A:R.92, A:Y.93, A:W.96, A:W.96, A:I.116, A:I.137, A:I.137, A:Y.141, A:F.145, A:F.145, A:I.149, A:I.149, A:V.182 Hydrogen bonds: A:Y.85, A:Y.112, A:N.126 Water bridges: A:R.92, A:R.92, A:T.128, A:T.128, A:T.128 Salt bridges: A:R.92, A:R.119 pi-Stacking: A:W.185 Metal complexes: A:H.120 HEM.3: 24 residues within 4Å: Chain B: L.70, Y.73, F.74, Y.85, V.89, R.92, Y.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 Ligands: CYN.4 32 PLIP interactions: 32 interactions with chain B, Hydrophobic interactions: B:Y.73, B:F.74, B:F.74, B:F.74, B:Y.85, B:V.89, B:R.92, B:Y.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:I.149, B:T.178, B:V.182 Hydrogen bonds: B:Y.112, B:N.126 Water bridges: B:R.92, B:R.92, B:T.128, B:D.129, B:D.129 Salt bridges: B:R.92, B:R.119 pi-Stacking: B:W.185 Metal complexes: B:H.120

2 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 4 residues within 4Å: Chain A: W.60, Y.61, Y.93 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CYN.4: 4 residues within 4Å: Chain B: W.60, Y.61, Y.93 Ligands: HEM.3 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: K.191, Y.192 Chain B: K.191, Y.192 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.192, A:Y.192 Water bridges: B:Y.192 GOL.6: 5 residues within 4Å: Chain B: D.51, Q.52, V.53, E.54, E.55 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.54, B:E.55 Water bridges: B:D.51, B:Q.52, B:E.55

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: G.193 Chain B: R.122, P.135, N.136 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.122, B:N.136, A:G.193 Salt bridges: B:R.122 SO4.8: 2 residues within 4Å: Chain B: R.103, S.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.104 Water bridges: B:D.106 Salt bridges: B:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tilleman, L. et al., Structural Bases for the Regulation of Co Binding in the Archaeal Protoglobin from Methanosarcina Acetivorans. Plos One (2015)

Release Date

2014-03-12

Peptides

PROTOGLOBIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTOGLOBIN