SMTL ID : 3zjq.1

M.acetivorans protoglobin in complex with nicotinamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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, V.182, W.185 Ligands: NCA.2 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:Y.73, A:F.74, A:Y.85, A:V.89, A:F.93, 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: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.4: 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, V.182, W.185 Ligands: NCA.5 27 PLIP interactions: 27 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: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:I.149, B:V.182 Hydrogen bonds: B:N.126 Water bridges: B:R.92, B:R.92, B:T.128, B:T.128, B:D.129 Salt bridges: B:R.92, B:R.119 pi-Stacking: B:W.185 Metal complexes: B:H.120

2 x NCA: NICOTINAMIDE(Non-covalent)

NCA.2: 9 residues within 4Å: Chain A: W.60, Y.61, V.64, F.74, V.89, F.93, F.145, I.149 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.61, A:F.74, A:V.89 Hydrogen bonds: A:W.60 pi-Stacking: A:F.93 NCA.5: 9 residues within 4Å: Chain B: W.60, Y.61, V.64, F.74, V.89, F.93, F.145, I.149 Ligands: HEM.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.61, B:F.74, B:V.89 Hydrogen bonds: B:W.60 pi-Stacking: B:F.93

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Y.9, Y.11, G.12, E.13, R.95, R.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.13, A:R.95, A:R.103, A:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pesce, A. et al., Structure and Haem-Distal Site Plasticity in Methanosarcina Acetivorans Protoglobin. Plos One (2013)

Release Date

2013-06-26

Peptides

PROTOGLOBIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTOGLOBIN

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