SMTL ID : 8rhi.1

Lytic Transglycosylase MltD of Pseudomonas aeruginosa in a ternary complex bound to Bulgecin A and chito-tetraose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 13 residues within 4Å: Chain A: F.54, V.87, I.88, E.89, S.90, A.91, A.96, S.98, Q.107, N.160, E.190, Y.194 Ligands: BLG.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.96 Hydrogen bonds: A:E.89, A:Q.107, A:N.160

1 x NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-NAG.2: 14 residues within 4Å: Chain B: W.47, F.54, Q.57, I.88, E.89, A.96, L.97, S.98, Q.107, N.160, E.190, Y.194, K.197 Ligands: BLG.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.96 Hydrogen bonds: B:E.89, B:Q.107, B:N.160

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

BLG.3: 17 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 Ligands: NAG-NAG.1, NAG-NAG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.108, A:Y.140, A:Y.159 Hydrogen bonds: A:E.89, A:E.89, A:S.98, A:R.99, A:I.109, A:Y.140, A:Y.140, A:Y.159, A:N.160, A:E.190 Water bridges: A:T.112, A:T.112, A:Y.140, A:E.163, A:E.163, A:G.164 Salt bridges: A:R.99 BLG.10: 16 residues within 4Å: Chain B: 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 Ligands: NAG-NAG-NAG-NAG.2 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.108, B:I.109, B:Y.140, B:Y.159 Hydrogen bonds: B:E.89, B:E.89, B:S.98, B:R.99, B:S.100, B:I.109, B:T.112, B:Y.140, B:Y.140, B:Y.159, B:N.160, B:E.190 Water bridges: B:E.163, B:E.163, B:G.164 Salt bridges: B:R.99

9 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: E.142, D.146 Chain B: E.142, D.146 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:E.142, A:D.146, B:E.142, B:D.146, B:D.146 ZN.5: 3 residues within 4Å: Chain A: H.8, H.10 Chain B: H.115 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.115, A:H.8, A:H.10, H2O.5 ZN.6: 3 residues within 4Å: Chain A: H.115, R.143 Chain B: H.9 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.9, A:H.115, H2O.3, H2O.3, H2O.5 ZN.7: 2 residues within 4Å: Chain A: H.9, D.27 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.9, A:D.27, A:D.27, H2O.1 ZN.8: 1 residues within 4Å: Chain A: H.145 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.145, H2O.1, H2O.3, H2O.5 ZN.9: 2 residues within 4Å: Chain A: E.171, E.174 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.171, A:E.171, A:E.174, A:E.174 ZN.11: 4 residues within 4Å: Chain B: H.8, H.10, E.14, D.27 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.8, B:H.10, B:E.14, B:D.27 ZN.12: 2 residues within 4Å: Chain B: H.145, W.152 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.145, H2O.5, H2O.6 ZN.13: 2 residues within 4Å: Chain B: D.245, D.247 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.245, B:D.245, B:D.247

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LysM peptidoglycan-binding domain-containing protein

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