SMTL ID : 8v8w.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: T.322, A.415, S.416, L.417, N.422, F.423 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.322 Hydrogen bonds: A:S.416, A:F.423

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

SO4.2: 3 residues within 4Å: Chain A: A.283, G.284, L.285 No protein-ligand interaction detected (PLIP)

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

MPD.3: 9 residues within 4Å: Chain A: E.309, G.312, R.314, H.335, V.336, D.337, G.405, D.406, M.407 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.407 Hydrogen bonds: A:D.337, A:G.405, A:G.405

2 x OXM: OXAMIC ACID(Non-covalent)

OXM.4: 7 residues within 4Å: Chain A: S.161, F.162, E.165, P.189, F.190, Q.194, Y.195 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.161, A:E.165, A:E.165, A:F.190 Water bridges: A:S.161 OXM.5: 6 residues within 4Å: Chain A: G.112, K.116, S.160, S.161, Y.195, K.199 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.116, A:S.161 Water bridges: A:S.160 Salt bridges: A:K.116, A:K.199

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 (Tetragonal 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

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