SMTL ID : 6rlg.1 (1 other biounit)

Crystal structure of LdtMt2 from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 4 residues within 4Å: Chain A: S.53, D.55, L.57, R.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.55

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 3 residues within 4Å: Chain A: D.107, G.108, H.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.107, A:D.107

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

EDO.3: 5 residues within 4Å: Chain A: E.160, H.161, F.162, I.238, W.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.160, A:F.162 EDO.4: 3 residues within 4Å: Chain A: S.253, P.258, V.259 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.259 EDO.5: 1 residues within 4Å: Chain A: P.344 No protein-ligand interaction detected (PLIP) EDO.6: 8 residues within 4Å: Chain A: V.22, D.23, A.24, P.25, E.63, Q.64, L.65, Y.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.65, A:L.65 EDO.7: 5 residues within 4Å: Chain A: N.42, N.44, R.46, R.69 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.42, A:N.44 EDO.8: 10 residues within 4Å: Chain A: N.42, R.46, P.47, V.48, E.63, L.65, G.66, R.69, Y.71 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.63, A:G.66, A:R.69, A:Y.71 Water bridges: A:R.69 EDO.9: 4 residues within 4Å: Chain A: N.74, T.85, R.86, Q.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.74, A:Q.87, A:Q.87 EDO.10: 9 residues within 4Å: Chain A: S.12, V.13, V.20, T.21, D.23, A.24, P.25, V.26, S.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.12, A:T.21, A:T.21, A:D.23 EDO.13: 7 residues within 4Å: Chain A: M.250, Y.265, T.267, W.287, S.298, H.299, C.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.267, A:H.299 Water bridges: A:S.298 EDO.14: 7 residues within 4Å: Chain A: Y.265, S.278, G.279, V.280, H.299, G.300, C.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.279 EDO.15: 6 residues within 4Å: Chain A: Y.148, P.333, G.334, I.335, I.343, Q.347 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.148, A:Y.148, A:G.334, A:I.335 Water bridges: A:Q.347

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 4 residues within 4Å: Chain A: I.135, K.136, I.137, F.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.135, A:I.137 NA.12: 4 residues within 4Å: Chain A: V.110, G.197, D.198, K.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.198, A:D.198, A:K.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Munnik, M. et al., Targeting the Mycobacterium tuberculosis transpeptidase LdtMt2with cysteine-reactive inhibitors including ebselen. Chem.Commun.(Camb.) (2019)

Release Date

2019-08-14

Peptides

L,D-transpeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L,D-transpeptidase 2

Related Entries With Identical Sequence