SMTL ID : 6o93.1

D-alanyl transferase DltD from Enterococcus faecalis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: V.109, K.110, K.264, W.265, D.266, Y.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.110, A:D.266, A:D.266, A:D.266 GOL.2: 7 residues within 4Å: Chain A: Y.128, K.156, D.157, K.158, V.159, L.160, Y.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.156, A:K.158, A:V.159, A:Y.180 GOL.3: 5 residues within 4Å: Chain A: V.159, E.162, S.176, Q.177, Y.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.176

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: N.115, D.116, P.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.115, A:D.116 Water bridges: A:N.115 PO4.5: 10 residues within 4Å: Chain A: S.46, S.47, A.76, G.77, T.78, Q.79, Q.106, W.107, H.349 Ligands: NA.10 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.46, A:S.46, A:S.47, A:S.47, A:G.77, A:W.107 Water bridges: A:Q.79, A:Q.79 PO4.6: 6 residues within 4Å: Chain A: F.246, Q.262, W.265, W.301, T.347, I.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.262, A:W.301, A:T.347 PO4.7: 2 residues within 4Å: Chain A: Q.174, R.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.175 Salt bridges: A:R.175

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

CL.8: 3 residues within 4Å: Chain A: R.66, Y.218, D.363 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: S.243, G.245, F.246 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: K.299, S.308, Q.309, D.310 Ligand excluded by PLIP

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

NA.10: 6 residues within 4Å: Chain A: S.46, S.47, E.48, S.104, H.349 Ligands: PO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.46, A:S.47, A:S.47, A:S.47, A:E.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shakhashiro, M. et al., D-alanyl transferase DltD from Enterococcus faecalis. To Be Published

Release Date

2019-03-27

Peptides

D-alanyl transferase DltD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D-alanyl transferase DltD