SMTL ID : 8rhf.2 (1 other biounit)

Lytic Transglycosylase MltD of Pseudomonas aeruginosa bound to the Natural Product Bulgecin A, with two LysM domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: T.112, H.115, Y.140 Ligands: BLG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.112

1 x BLG: 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE(Non-covalent)

BLG.2: 18 residues within 4Å: Chain A: E.89, S.98, R.99, S.100, A.102, Q.107, F.108, I.109, T.112, Y.140, Y.159, N.160, A.161, G.162, E.190, Y.194 Ligands: PEG.1, ZN.7 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.108, A:Y.140, A:Y.159 Hydrogen bonds: A:S.98, A:S.98, A:R.99, A:S.100, A:S.100, A:I.109, A:Y.140, A:Y.140, A:Y.159, A:N.160, A:E.190, A:Y.194 Water bridges: A:E.163, A:E.163, A:E.163, A:E.163, A:G.164

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: E.142, D.146 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.142, A:D.146, A:D.146 ZN.4: 2 residues within 4Å: Chain A: H.6, H.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.6, A:H.9 ZN.5: 4 residues within 4Å: Chain A: H.8, H.10, E.14, D.27 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.8, A:H.10, A:E.14, A:E.14, A:D.27 ZN.6: 2 residues within 4Å: Chain A: H.145, W.152 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.145 ZN.7: 3 residues within 4Å: Chain A: E.89, Q.107 Ligands: BLG.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.89, H2O.4, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miguel-Ruano, V. et al., Structural characterization of lytic transglycosylase MltD of Pseudomonas aeruginosa, a target for the natural product bulgecin A. Int.J.Biol.Macromol. (2024)

Release Date

2024-04-17

Peptides

LysM peptidoglycan-binding domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LysM peptidoglycan-binding domain-containing protein

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