SMTL ID : 3jva.1

Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-octamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: E.57, T.58, G.61, T.62 Chain E: G.56, E.57, T.58, G.61, T.62 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:G.56, E:T.58, E:T.58, E:T.62, A:T.58, A:T.58 Water bridges: E:E.57 GOL.4: 6 residues within 4Å: Chain B: G.165, I.166, W.194, D.198, K.201, A.202 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.166, B:D.198 Water bridges: B:G.163, B:G.165 GOL.5: 8 residues within 4Å: Chain A: M.1, N.77, K.113 Chain B: L.116, P.117, Y.119, Q.120, E.346 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.119, B:Q.120, A:M.1, A:M.1, A:N.77, A:K.113, A:K.113 GOL.6: 6 residues within 4Å: Chain B: F.53, I.54, K.159, D.189, K.264, C.292 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.159, B:K.159, B:C.292 Water bridges: B:K.264, B:K.264, B:C.292, B:A.294 GOL.14: 4 residues within 4Å: Chain F: I.54, K.159, K.264, C.292 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.189 Water bridges: F:K.264, F:K.264, F:K.264, F:K.264, F:C.292

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.161, D.189, E.215, D.240 Ligands: SO4.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.189, A:E.215, A:D.240, H2O.1, H2O.1 MG.7: 3 residues within 4Å: Chain B: D.189, E.215, D.240 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.189, B:E.215, B:D.240, H2O.4, H2O.4, H2O.4 MG.8: 5 residues within 4Å: Chain C: D.189, E.215, D.240, E.241 Ligands: SO4.10 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.189, C:E.215, C:D.240, H2O.10, H2O.10, H2O.13 MG.11: 3 residues within 4Å: Chain D: D.189, E.215, D.240 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.189, D:E.215, D:D.240, H2O.13, H2O.13, H2O.13 MG.12: 5 residues within 4Å: Chain E: K.159, D.189, E.215, D.240 Ligands: SO4.13 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.189, E:E.215, E:D.240, H2O.18, H2O.18 MG.15: 3 residues within 4Å: Chain F: D.189, E.215, D.240 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.189, F:E.215, F:D.240, H2O.22, H2O.22, H2O.22 MG.16: 5 residues within 4Å: Chain G: D.189, E.215, D.240, E.241 Ligands: SO4.17 6 PLIP interactions: 3 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.189, G:E.215, G:D.240, H2O.27, H2O.27, H2O.27 MG.18: 3 residues within 4Å: Chain H: D.189, E.215, D.240 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.189, H:E.215, H:D.240, H2O.30, H2O.30, H2O.30

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

SO4.3: 9 residues within 4Å: Chain A: K.159, K.161, D.189, E.215, D.240, K.264, C.292, D.318 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.318 Water bridges: A:K.161, A:N.191, A:N.262, A:K.264 Salt bridges: A:K.159, A:K.161, A:K.264 SO4.9: 6 residues within 4Å: Chain C: G.56, T.58, G.61, T.62 Chain G: T.58, G.61 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:T.58, G:G.61, C:T.58, C:T.58 SO4.10: 7 residues within 4Å: Chain C: K.159, K.161, D.189, K.264, C.292, D.318 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:D.189 Water bridges: C:T.134, C:T.134, C:K.159, C:K.264, C:K.264, C:K.264, C:K.264, C:K.264, C:K.264 Salt bridges: C:K.159, C:K.161, C:K.264 SO4.13: 9 residues within 4Å: Chain E: K.159, K.161, D.189, E.215, D.240, K.264, C.292, D.318 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:D.189, E:D.318 Water bridges: E:T.134, E:N.191, E:N.191, E:N.262, E:K.264 Salt bridges: E:K.159, E:K.161, E:K.264 SO4.17: 6 residues within 4Å: Chain G: K.159, K.161, D.189, K.264, C.292 Ligands: MG.16 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:D.318 Water bridges: G:K.159, G:K.159, G:K.264, G:K.264 Salt bridges: G:K.159, G:K.161, G:K.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukk, T. et al., Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2010-08-11

Peptides

Dipeptide Epimerase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Dipeptide Epimerase

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