SMTL ID : 6vr8.1

Structure of a pseudomurein peptide ligase type E from Methanothermus fervidus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: N.120, G.121, K.122, S.123, T.124, R.332, F.346 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.121, A:G.121, A:S.123, A:T.124 Water bridges: A:K.122, A:N.301, A:N.301 Salt bridges: A:R.332

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.124, N.301, R.332 Ligands: PO4.1 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: H.131, T.134, H.135, K.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.134 EDO.4: 4 residues within 4Å: Chain A: H.48, I.154, W.184, L.185 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.184, A:L.185

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: R.375, R.378, Q.465 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.465 Water bridges: A:R.375, A:R.375 Salt bridges: A:R.375, A:R.378 SO4.6: 4 residues within 4Å: Chain A: T.35, L.36, G.37, R.47 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.36, A:G.37 Water bridges: A:T.35, A:T.35 Salt bridges: A:R.47 SO4.7: 4 residues within 4Å: Chain A: H.439, K.440, K.441, T.444 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.440, A:K.441, A:T.444, A:T.444 Water bridges: A:F.438 Salt bridges: A:H.439

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.8: 9 residues within 4Å: Chain A: Q.69, K.91, I.92, E.93, W.184, R.187, L.188, M.189, K.190 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.69, A:Q.69, A:E.93, A:E.93, A:R.187, A:K.190 Water bridges: A:W.184 Salt bridges: A:K.91, A:K.91, A:K.190, A:K.190 pi-Stacking: A:W.184 pi-Cation interactions: A:K.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Subedi, B.P. et al., Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases. Microbiology (Reading, Engl.) (2022)

Release Date

2021-08-11

Peptides

Mur ligase middle domain protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

Mur ligase middle domain protein

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