SMTL ID : 4q6j.1

Crystal Structure of EAL domain Protein from Listeria monocytogenes EGD-e

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: Q.83, K.246, V.252 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.252, A:V.252 Water bridges: A:K.246, A:K.246, A:K.246, A:K.246 Salt bridges: A:K.246 PO4.11: 1 residues within 4Å: Chain B: R.189 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.189 PO4.18: 3 residues within 4Å: Chain C: Q.83, K.246, V.252 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:V.252, C:V.252 Water bridges: C:K.246, C:K.246, C:K.246, C:K.246 Salt bridges: C:K.246 PO4.28: 1 residues within 4Å: Chain D: R.189 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.189

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

EDO.2: 7 residues within 4Å: Chain A: K.27, I.36, S.89, E.123, I.174, V.210, Y.230 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: N.82, H.115, K.117 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Q.70, D.71, A.74, E.75, Y.104, F.107, Y.111 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: I.127, E.128, D.155, D.156 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: W.12 Chain B: A.183, L.184, D.216, Q.219 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: S.8, T.9, W.12 Chain B: M.179, Q.219 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: Q.25, G.213, E.215, G.233, Y.234 Chain B: M.4, S.8 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain B: Q.25, G.213, V.214, E.215, G.233, Y.234 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: K.27, I.36, E.123, I.174, V.210, Y.230 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: F.107, D.110, Y.111, E.114, H.115 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain B: Q.70, D.71, A.74, E.75, Y.104, F.107, L.108, Y.111 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: I.127, E.128, D.155, D.156 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: Y.234, S.237, R.238 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain C: K.27, I.36, S.89, E.123, I.174, V.210, Y.230 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain C: N.82, H.115, K.117 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain C: Q.70, D.71, A.74, E.75, Y.104, F.107, Y.111 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain C: I.127, E.128, D.155, D.156 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain C: W.12 Chain D: A.183, L.184, D.216, Q.219 Ligands: EDO.25 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: S.8, T.9, W.12 Chain D: M.179, Q.219 Ligands: EDO.24 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: Q.25, G.213, E.215, G.233, Y.234 Chain D: M.4, S.8 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain D: Q.25, G.213, V.214, E.215, G.233, Y.234 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain D: K.27, I.36, E.123, I.174, V.210, Y.230 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: F.107, D.110, Y.111, E.114, H.115 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain D: Q.70, D.71, A.74, E.75, Y.104, F.107, L.108, Y.111 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain D: I.127, E.128, D.155, D.156 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain D: Y.234, S.237, R.238 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: A.183, L.184, D.216, Q.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.184 Water bridges: A:L.184, A:L.185 GOL.23: 4 residues within 4Å: Chain C: A.183, L.184, D.216, Q.219 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.184 Water bridges: C:L.184, C:L.185, C:D.216

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.17: 7 residues within 4Å: Chain B: A.100, S.101, S.102, T.103 Chain D: S.101, T.103 Ligands: ACY.34 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:T.103, B:S.102, B:T.103, B:T.103 Water bridges: D:S.101, D:S.101, B:A.100 ACY.34: 7 residues within 4Å: Chain B: S.101, T.103 Chain D: A.100, S.101, S.102, T.103 Ligands: ACY.17 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Water bridges: B:S.101, B:S.101, D:A.100 Hydrogen bonds: D:S.102, D:T.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of EAL domain Protein from Listeria monocytogenes EGD-e. To be Published

Release Date

2014-05-07

Peptides

Lmo0131 protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Lmo0131 protein