SMTL ID : 8g6p.1

Crystal structure of Mycobacterium thermoresistibile MurE in complex with ADP and 2,6-Diaminopimelic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Ligands: GOL.6 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain A: H.223 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:H.223, H2O.2, H2O.3, H2O.4, H2O.11, H2O.14 MG.11: 4 residues within 4Å: Chain A: T.133, T.155, E.195 Ligands: ADP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.133, A:E.195, H2O.18

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: A.281, D.282, V.284, V.301, D.302, P.303 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.303 GOL.3: 7 residues within 4Å: Chain A: A.276, T.277, G.278, A.285, E.286, V.288, R.317 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.276, A:G.278, A:R.317 Water bridges: A:T.277, A:D.287 GOL.5: 5 residues within 4Å: Chain A: P.243, C.248, A.249, E.250, H.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.249 Water bridges: A:P.243, A:C.248 GOL.6: 8 residues within 4Å: Chain A: Y.137, V.156, G.157, V.158, R.159, D.164, P.350 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.137, A:V.158, A:D.164 Water bridges: A:R.159, A:D.164 GOL.7: 6 residues within 4Å: Chain A: R.458, D.462, A.502, A.503, A.506, R.507 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.458, A:D.462, A:A.503, A:A.503 GOL.8: 5 residues within 4Å: Chain A: P.7, S.8, V.183, D.186, R.187 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.8, A:S.8, A:D.186, A:D.186 Water bridges: A:D.9

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 20 residues within 4Å: Chain A: G.128, T.129, S.130, G.131, K.132, T.133, T.134, E.195, N.218, F.318, N.322, R.352, L.353, D.367, Y.368, A.369, A.374, A.377, V.378 Ligands: MG.11 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.130, A:G.131, A:K.132, A:T.133, A:T.133, A:T.133, A:T.134, A:T.134, A:N.218, A:N.322, A:N.322, A:D.367, A:Y.368, A:A.369 Water bridges: A:T.129, A:K.132 Salt bridges: A:K.132, A:R.352 pi-Stacking: A:F.318, A:F.318

1 x API: 2,6-DIAMINOPIMELIC ACID(Non-covalent)

API.9: 9 residues within 4Å: Chain A: Y.368, H.370, G.397, R.400, D.424, N.425, R.427, G.478, E.482 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:H.370 Hydrogen bonds: A:G.397, A:D.424, A:D.424, A:N.425, A:E.482 Water bridges: A:R.400, A:K.404, A:K.404, A:R.427, A:R.427, A:E.482, A:E.482 Salt bridges: A:R.400, A:R.400, A:R.427, A:R.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rossini, N.O. et al., The crystal structure of Mycobacterium thermoresistibile MurE ligase reveals the binding mode of the substrate m-diaminopimelate. J.Struct.Biol. (2023)

Release Date

2023-04-05

Peptides

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase