SMTL ID : 7m5h.1

Crystal structure of conserved protein from Enterococcus faecalis V583

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 12 residues within 4Å: Chain A: Y.8, A.10, G.11, L.13, F.14, D.63, D.83, G.85, V.86, E.89 Chain B: N.133 Ligands: EDO.3 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.11, A:D.63, A:D.63, A:D.83, A:V.86, B:N.133 Water bridges: A:F.9, A:G.11 GOL.4: 2 residues within 4Å: Chain A: Y.94 Chain B: K.96 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.96, B:K.96 Water bridges: A:Y.94, A:G.97 GOL.5: 12 residues within 4Å: Chain A: N.133 Chain B: Y.8, A.10, G.11, L.13, F.14, D.63, D.83, G.85, V.86, E.89 Ligands: EDO.2 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.11, B:D.63, B:D.83, A:N.133 Water bridges: B:F.9, B:G.11 GOL.7: 12 residues within 4Å: Chain C: Y.8, A.10, G.11, L.13, F.14, D.63, D.83, G.85, V.86, E.89 Chain D: N.133 Ligands: EDO.9 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.11, C:D.63, C:D.63, C:D.83, C:V.86, D:N.133 Water bridges: C:F.9, C:G.11 GOL.10: 2 residues within 4Å: Chain C: Y.94 Chain D: K.96 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:Y.94, C:G.97 Hydrogen bonds: D:K.96, D:K.96 GOL.11: 12 residues within 4Å: Chain C: N.133 Chain D: Y.8, A.10, G.11, L.13, F.14, D.63, D.83, G.85, V.86, E.89 Ligands: EDO.8 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:N.133, D:G.11, D:D.63, D:D.83 Water bridges: D:F.9, D:G.11

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: N.133, Y.135 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.133, A:N.133 Water bridges: A:L.134 EDO.3: 4 residues within 4Å: Chain A: F.14 Chain B: N.133, Y.135 Ligands: GOL.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.133, B:N.133 EDO.6: 3 residues within 4Å: Chain A: K.96 Chain B: Y.94, A.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.96 EDO.8: 3 residues within 4Å: Chain C: N.133, Y.135 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.133, C:N.133 Water bridges: C:L.134 EDO.9: 4 residues within 4Å: Chain C: F.14 Chain D: N.133, Y.135 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.133, D:N.133 EDO.12: 3 residues within 4Å: Chain C: K.96 Chain D: Y.94, A.95 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Crystal structure of conserved protein from Enterococcus faecalis V583. To Be Published

Release Date

2021-04-07

Peptides

Nucleoside 2-deoxyribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Nucleoside 2-deoxyribosyltransferase