SMTL ID : 7pj6.1

Crystal structure of catalytic domain of LytB (E585Q) from Streptococcus pneumoniae in complex with NAG-NAM-NAG-NAM-NAG peptidolycan analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x 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

NAG-AMU-NAG-AMU-NAG.1: 25 residues within 4Å: Chain A: T.11, Y.24, V.84, A.88, I.90, L.179, Q.180, N.182, S.186, I.188, G.197, T.199, A.200, Y.201, D.202, P.205, W.225, Y.230, E.248, Y.249, A.250, S.251, D.252, K.258 Ligands: PEG.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.225, A:Y.249, A:Y.24 Hydrogen bonds: A:Y.24, A:T.199, A:A.200, A:D.202, A:D.202, A:Y.230, A:Y.230, A:Y.249

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 5 residues within 4Å: Chain A: N.149, R.185, S.186, K.187, K.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.190

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 5 residues within 4Å: Chain A: E.137, K.140, L.144, K.269, L.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.140

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 6 residues within 4Å: Chain A: N.229, Y.230, R.233, R.235, E.248 Ligands: NAG-AMU-NAG-AMU-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.233

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain A: D.16, D.18, E.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:D.18, A:E.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Caballero, S. et al., Molecular basis of the final step of cell division in Streptococcus pneumoniae. Cell Rep (2023)

Release Date

2022-09-07

Peptides

Putative endo-beta-N-acetylglucosaminidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Putative endo-beta-N-acetylglucosaminidase

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