SMTL ID : 5dc2.1 (1 other biounit)

X-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDUCT OF L,D-TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

1 x 58U: (4S)-4-methyl-2,5,7-trioxoheptanoic acid(Covalent)

58U.1: 12 residues within 4Å: Chain A: M.248, Y.263, G.277, H.281, W.285, T.295, S.296, H.297, G.298, C.299, N.301 Ligands: EDO.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.297 Hydrogen bonds: A:H.297, A:G.298, A:C.299, A:N.301 Salt bridges: A:H.297

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.44, R.67 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.67, A:R.67, A:R.67 Salt bridges: A:R.67 SO4.3: 2 residues within 4Å: Chain A: R.242, R.316 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.242 Water bridges: A:E.107, A:E.107, A:R.316 Salt bridges: A:R.316 SO4.4: 7 residues within 4Å: Chain A: M.102, E.113, A.116, R.154, Y.275, R.316, L.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.275, A:R.316 Salt bridges: A:R.154 SO4.5: 2 residues within 4Å: Chain A: S.51, P.52 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.56 SO4.6: 4 residues within 4Å: Chain A: N.40, N.42, R.44 Ligands: SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.40, A:N.42 Water bridges: A:R.67, A:R.67 Salt bridges: A:R.67

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

PEG.7: 2 residues within 4Å: Chain A: N.149, N.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.150, A:N.150 PEG.8: 4 residues within 4Å: Chain A: G.31, V.32, L.76, G.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.78 PEG.9: 8 residues within 4Å: Chain A: E.130, A.144, F.145, W.346, R.347, A.348, G.349 Ligands: PEG.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.145, A:R.347 Water bridges: A:N.350 PEG.10: 7 residues within 4Å: Chain A: I.133, K.134, I.135, G.143, W.155 Ligands: PEG.9, PGE.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.135

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

PGE.11: 5 residues within 4Å: Chain A: E.158, H.159, F.160, E.197, I.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.160 Water bridges: A:E.321 PGE.12: 8 residues within 4Å: Chain A: K.134, I.135, T.136, T.137, P.140, V.141, W.155 Ligands: PEG.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.134, A:K.134, A:T.137

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: S.303, P.304, S.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.303, A:S.305 GOL.14: 6 residues within 4Å: Chain A: R.126, W.147, L.148, N.149, N.150, N.350 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.126, A:R.126, A:N.150, A:N.350 GOL.15: 7 residues within 4Å: Chain A: V.20, D.21, A.22, P.23, E.61, Q.62, L.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.63, A:L.63 Water bridges: A:E.61

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

EDO.16: 6 residues within 4Å: Chain A: Y.263, S.276, G.277, H.297, G.298 Ligands: 58U.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.263, A:G.277, A:C.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bianchet, M.A. et al., Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem. BMC Biochem. (2017)

Release Date

2016-10-05

Peptides

L,D-transpeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L,D-transpeptidase 2

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