SMTL ID : 3zji.1

Tyr(61)B10Ala 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: 24 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 Ligands: CYN.2 33 PLIP interactions: 33 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:F.93, A:F.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:T.178, 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.5: 24 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 Ligands: CYN.6 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:R.92, 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:I.149, B:T.178, B:V.182 Hydrogen bonds: 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, F.93 Ligands: HEM.1, GOL.3 No protein-ligand interaction detected (PLIP) CYN.6: 4 residues within 4Å: Chain B: W.60, F.93 Ligands: HEM.5, GOL.7 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: W.60, F.74, L.86, V.89, R.90, F.93 Ligands: CYN.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.61, A:L.86, A:R.90 GOL.4: 4 residues within 4Å: Chain A: G.12, T.14, N.16, D.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.111, A:D.111 Water bridges: A:T.14, A:Q.107 GOL.7: 8 residues within 4Å: Chain B: W.60, A.61, F.74, L.86, V.89, R.90, F.93 Ligands: CYN.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.86, B:R.90 Water bridges: B:A.61, B:A.61, B:G.65, B:R.90

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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