SMTL ID : 2mtz.1

Haddock model of Bacillus subtilis L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide

Coordinates

PDB Format Compare

Method

SOLID-STATE NMR

Oligo State

monomer

Ligands

6 x ALA- FGA- API- DAL: intact bacterial peptidoglycan(Non-functional Binders)(Non-covalent)

ALA-FGA-API-DAL.1: 1 residues within 4Å: Ligands: AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.2 ALA-FGA-API-DAL.2: 3 residues within 4Å: Chain A: Y.55 Ligands: AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7, AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7 No protein-ligand interaction detected (PLIP) ALA-FGA-API-DAL.3: 4 residues within 4Å: Chain A: E.97 Ligands: AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7, AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7, AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.97 ALA-FGA-API-DAL.4: 3 residues within 4Å: Chain A: Q.11, G.12 Ligands: AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7 No protein-ligand interaction detected (PLIP) ALA-FGA-API-DAL.5: 14 residues within 4Å: Chain A: D.21, R.23, F.111, W.115, Q.121, H.122, H.126, C.142 Ligands: ALA-FGA-API-DAL.6, ALA-FGA-API-DAL.6, AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7, AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7, AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7, AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.111, A:W.115, A:Q.121, A:H.122 Hydrogen bonds: A:Q.121, A:Q.121, A:Q.121, A:Q.121, A:H.122 Salt bridges: A:H.126 ALA-FGA-API-DAL.6: 4 residues within 4Å: Chain A: R.23, Q.104 Ligands: ALA-FGA-API-DAL.5, AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.104 Salt bridges: A:R.23

1 x AMU- NAG- AMU- NAG- AMU- NAG- AMU- NAG- AMU- NAG- AMU- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid

AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG-AMU-NAG.7: 36 residues within 4Å: Chain A: R.2, K.3, L.4, L.5, T.6, Y.7, Q.8, K.10, Q.11, D.13, A.20, D.21, S.45, V.47, D.53, Y.55, I.89, T.93, P.94, T.95, E.97, Y.99, K.120, Q.121 Ligands: ALA-FGA-API-DAL.1, ALA-FGA-API-DAL.2, ALA-FGA-API-DAL.2, ALA-FGA-API-DAL.3, ALA-FGA-API-DAL.3, ALA-FGA-API-DAL.4, ALA-FGA-API-DAL.4, ALA-FGA-API-DAL.5, ALA-FGA-API-DAL.5, ALA-FGA-API-DAL.5, ALA-FGA-API-DAL.6, ALA-FGA-API-DAL.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.47 Hydrogen bonds: A:K.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schanda, P. et al., Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. J.Am.Chem.Soc. (2014)

Release Date

2015-01-14

Peptides

Putative L,D-transpeptidase YkuD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Putative L,D-transpeptidase YkuD

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