SMTL ID : 8vw1.1

Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ADP bound)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: S.113, N.114, G.115, K.116, S.117, T.118, E.158, N.179, H.268, N.272, R.303, F.304, D.318, K.320, A.321, S.326, A.329 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.115, A:K.116, A:S.117, A:S.117, A:T.118, A:N.179, A:N.272, A:N.272, A:D.318, A:K.320, A:S.326 Water bridges: A:T.118, A:N.269, A:K.320, A:K.320 Salt bridges: A:K.116, A:R.303, A:K.320, A:K.320 pi-Stacking: A:H.268

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

MG.2: 3 residues within 4Å: Chain A: S.117, E.158 Ligands: ADP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.158, H2O.7 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: D.36, T.37 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: Q.387, T.388 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain A: A.415, S.416, F.423 No protein-ligand interaction detected (PLIP)

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 4 residues within 4Å: Chain A: A.213, S.230, M.235, G.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.230 Water bridges: A:A.213

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.9: 7 residues within 4Å: Chain A: L.164, T.167, S.168, S.169, L.170, R.201, E.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seibold, S. et al., Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ADP bound). To be published

Release Date

2024-02-14

Peptides

UDP-N-acetylmuramoylalanine--D-glutamate ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylmuramoylalanine--D-glutamate ligase

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