SMTL ID : 2veb.1

High resolution structure of protoglobin from Methanosarcina acetivorans C2A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 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: OXY.5 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:Y.73, 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:Y.141, A:F.145, A:F.145, A:I.149, A:V.182 Hydrogen bonds: 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.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, I.149, V.182, W.185 Ligands: OXY.10 28 PLIP interactions: 28 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:Y.141, B:F.145, B:F.145, B:I.149, B:V.182 Hydrogen bonds: B:Y.85, 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

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: G.12, E.13, T.14, E.15, N.16, A.108, D.111 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.12, A:G.12, A:T.14, A:E.15, A:N.16, A:D.111 PO4.3: 5 residues within 4Å: Chain A: Y.72, Y.73, V.134, P.135, N.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.136 Water bridges: A:Y.72, A:Y.72, A:R.122 PO4.7: 7 residues within 4Å: Chain B: G.12, E.13, T.14, E.15, N.16, A.108, D.111 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.12, B:G.12, B:T.14, B:E.15, B:N.16 PO4.8: 5 residues within 4Å: Chain B: Y.72, Y.73, V.134, P.135, N.136 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.72, B:N.136 Water bridges: B:Y.72, B:Y.73, B:R.122

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Y.187, P.188, V.190, Y.192 Chain B: K.191 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.191, A:V.190 Water bridges: B:K.191 GOL.9: 5 residues within 4Å: Chain A: K.191 Chain B: Y.187, P.188, V.190, Y.192 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.190, A:K.191 Water bridges: B:Y.187, A:K.191

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 2 residues within 4Å: Chain A: F.93 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) OXY.10: 2 residues within 4Å: Chain B: F.93 Ligands: HEM.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nardini, M. et al., Archaeal Protoglobin Structure Indicates New Ligand Diffusion Paths and Modulation of Haem-Reactivity. Embo Rep. (2008)

Release Date

2008-01-22

Peptides

PROTOGLOBIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PROTOGLOBIN

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