SMTL ID : 8v8y.1

Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Orthorhombic P form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: S.21, R.122, E.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.123 Water bridges: A:A.23

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: G.136, K.137, S.138, T.139, R.324 Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: T.343, A.436, S.437, F.444 Ligand excluded by PLIP

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

MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: D.44 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: R.422 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.422

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

MPD.8: 4 residues within 4Å: Chain A: A.234, S.251, M.256, G.257 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.234 Hydrogen bonds: A:S.251

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 (Orthorhombic P form). To be published

Release Date

2023-12-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylmuramoylalanine--D-glutamate ligase