SMTL ID : 8vw0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 15 residues within 4Å: Chain A: N.114, G.115, K.116, S.117, T.118, N.179, H.268, N.272, R.303, F.304, D.318, K.320, A.321, S.326, A.329 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.115, A:K.116, A:S.117, A:S.117, A:S.117, A:T.118, A:N.179, A:N.272, A:N.272, A:K.320, A:S.326 Water bridges: A:N.269 Salt bridges: A:R.303 pi-Stacking: A:H.268

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: D.36, T.37 No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: Q.387, T.388 No protein-ligand interaction detected (PLIP) CA.5: 3 residues within 4Å: Chain A: A.415, S.416, F.423 No protein-ligand interaction detected (PLIP) CA.6: 6 residues within 4Å: Chain A: G.13, L.14, G.15, T.17, G.18, S.72 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain A: D.373 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain A: Q.387 No protein-ligand interaction detected (PLIP)

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

MPD.9: 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:A.213, A:S.230

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

DMS.10: 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 (AMP 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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