SMTL ID : 3zh0.1 (1 other biounit)

Functional and structural role of the N-terminal extension in Methanosarcina acetivorans protoglobin

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: 23 residues within 4Å: Chain A: L.51, Y.54, F.55, Y.66, V.70, R.73, F.74, W.77, Y.93, I.97, R.100, H.101, K.106, N.107, I.118, Y.122, L.123, F.126, I.127, I.130, V.163, W.166 Ligands: FMT.2 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:Y.54, A:F.55, A:Y.66, A:V.70, A:R.73, A:F.74, A:F.74, A:W.77, A:W.77, A:I.97, A:I.118, A:I.118, A:Y.122, A:F.126, A:F.126, A:I.130, A:I.130, A:V.163, A:W.166 Hydrogen bonds: A:Y.93, A:N.107 Water bridges: A:R.73, A:R.73, A:R.76, A:T.109, A:T.109, A:T.109 Salt bridges: A:R.73, A:R.73, A:R.100 Metal complexes: A:H.101 HEM.5: 23 residues within 4Å: Chain B: L.51, Y.54, F.55, Y.66, V.70, R.73, F.74, W.77, Y.93, I.97, R.100, H.101, K.106, N.107, I.118, Y.122, L.123, F.126, I.127, I.130, V.163, W.166 Ligands: FMT.6 32 PLIP interactions: 32 interactions with chain B, Hydrophobic interactions: B:Y.54, B:F.55, B:F.55, B:F.55, B:Y.66, B:V.70, B:R.73, B:F.74, B:F.74, B:W.77, B:W.77, B:I.97, B:I.118, B:I.118, B:Y.122, B:L.123, B:F.126, B:F.126, B:I.130, B:I.130, B:V.163 Hydrogen bonds: B:Y.66, B:R.73, B:N.107 Water bridges: B:R.73, B:T.109, B:D.110, B:D.110 Salt bridges: B:R.73, B:R.100 pi-Stacking: B:W.166 Metal complexes: B:H.101

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: W.41, Y.42, V.70, F.74 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.42, A:Y.42 FMT.6: 4 residues within 4Å: Chain B: W.41, Y.42, F.74 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.42

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.32, Q.33, V.34, E.35, E.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.35, A:E.36, A:E.36 GOL.4: 6 residues within 4Å: Chain A: K.7, K.10, F.15, T.16, A.17, E.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.10, A:F.15, A:E.20 GOL.7: 3 residues within 4Å: Chain B: M.1, D.92, Y.168 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.1, B:M.1, B:D.92, B:D.92, B:Y.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciaccio, C. et al., Functional and Structural Role of the N-Terminal Extension in Methanosarcina Acetivorans Protoglobin. Biochim.Biophys.Acta (2013)

Release Date

2013-03-27

Peptides

PROTOGLOBIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTOGLOBIN

Related Entries With Identical Sequence