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

Phe(93)E11Leu mutation of M.acetivorans protoglobin in complex with cyanide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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, L.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 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:L.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: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:T.128, A:D.129 Salt bridges: A:R.92, A:R.119 pi-Stacking: A:W.185 Metal complexes: A:H.120 HEM.7: 24 residues within 4Å: Chain B: L.70, Y.73, F.74, Y.85, V.89, R.92, L.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.8 31 PLIP interactions: 31 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:L.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: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: 2 residues within 4Å: Chain A: W.60 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CYN.8: 2 residues within 4Å: Chain B: W.60 Ligands: HEM.7 No protein-ligand interaction detected (PLIP)

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

EPE.3: 8 residues within 4Å: Chain A: E.39, I.42, Q.43, S.101, N.102, R.103, S.104, Y.105 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.43, A:R.103 Water bridges: A:Y.105 Salt bridges: A:E.39, A:E.39 EPE.9: 8 residues within 4Å: Chain B: E.39, I.42, Q.43, S.101, N.102, R.103, S.104, Y.105 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.43, B:R.103 Water bridges: B:Y.105 Salt bridges: B:E.39, B:E.39

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: N.126, Q.127, N.130, V.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.126, A:V.131 GOL.5: 6 residues within 4Å: Chain A: S.76, P.77, N.82, K.84, V.131, E.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.76, A:N.82, A:E.132 Water bridges: A:N.130 GOL.10: 4 residues within 4Å: Chain B: N.126, Q.127, N.130, V.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.126, B:V.131 GOL.11: 6 residues within 4Å: Chain B: S.76, P.77, N.82, K.84, V.131, E.132 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.76, B:N.82, B:E.132, B:E.132 Water bridges: B:N.130

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.6: 4 residues within 4Å: Chain A: E.50, R.95, L.98, N.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.102 Water bridges: A:R.95, A:L.98 IPA.12: 4 residues within 4Å: Chain B: E.50, R.95, L.98, N.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.102 Water bridges: B:R.95, B:L.98

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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