SMTL ID : 3zjm.1 (1 other biounit)

Ile(149)G11Phe mutation of M.acetivorans protoglobin in complex with cyanide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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, T.178, V.182, W.185 Ligands: CYN.2 30 PLIP interactions: 30 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: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:T.178, A:V.182 Hydrogen bonds: A:Y.85, A:N.126 Water bridges: A:R.92, A:R.92, A:T.128, 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.6: 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, T.178, V.182, W.185 Ligands: CYN.7 30 PLIP interactions: 30 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:F.93, B:F.93, B:W.96, B:W.96, B:I.116, B:I.137, B:I.137, B:Y.141, B:L.142, B:F.145, B:F.145, 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:T.128, B:T.128 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, F.93 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CYN.7: 4 residues within 4Å: Chain B: W.60, Y.61, F.93 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.61

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.191, Y.192 Chain B: K.191 Ligands: GOL.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.192 Hydrogen bonds: A:Y.192 GOL.4: 3 residues within 4Å: Chain A: T.59, T.152 Chain B: M.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.59 GOL.8: 4 residues within 4Å: Chain A: K.191 Chain B: K.191, Y.192 Ligands: GOL.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.192 Water bridges: A:Y.192 GOL.9: 3 residues within 4Å: Chain A: M.33 Chain B: T.59, T.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.59, B:T.152

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 9 residues within 4Å: Chain A: E.39, I.42, Q.43, T.100, S.101, N.102, R.103, S.104, Y.105 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.103 Water bridges: A:Q.43, A:Y.105 Salt bridges: A:E.39 EPE.10: 9 residues within 4Å: Chain B: E.39, I.42, Q.43, T.100, S.101, N.102, R.103, S.104, Y.105 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.103 Water bridges: B:Q.43, B:Y.105 Salt bridges: B:E.39

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
C

B
C

PROTOGLOBIN

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