SMTL ID : 7lgp.1

DapE enzyme from Shigella flexneri

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.69, D.102, E.136, E.137, E.165 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, A:D.102, A:E.165, A:E.165, H2O.3 ZN.10: 5 residues within 4Å: Chain B: H.69, D.102, E.136, E.137, E.165 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.69, B:D.102, B:E.165, B:E.165, H2O.14

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

CL.2: 5 residues within 4Å: Chain A: C.6, P.7, V.8, I.9, Q.363 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: A.49, D.50, T.51, N.142 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: H.121, P.122, N.123, H.124 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: R.181, P.230 Chain B: P.200 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: F.117, H.121, Q.370, E.374 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: G.293, Q.294, R.331, F.332, R.335 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: Q.194, P.250, G.251 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: C.6, P.7, V.8, I.9, Q.363 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: Q.120, H.121, Q.370, E.374 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: Q.194, P.250, G.251 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: G.293, Q.294, R.331, R.335 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: G.301, K.302, Q.339 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: Q.37, T.42, V.43 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: H.121, P.122, N.123, H.124 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: Q.235 Chain B: D.204, N.205 Ligand excluded by PLIP

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

NA.9: 2 residues within 4Å: Chain A: Q.60, T.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.60, A:T.125 NA.19: 2 residues within 4Å: Chain B: Q.60, T.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.60 NA.20: 2 residues within 4Å: Chain B: N.226, F.229 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.226, B:N.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., DapE enzyme from Shigella flexneri. To Be Published

Release Date

2021-01-27

Peptides

Succinyl-diaminopimelate desuccinylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Succinyl-diaminopimelate desuccinylase