SMTL ID : 5org.1

Structure of the periplasmic binding protein (PBP) OccJ from A. tumefaciens B6 in complex with octopine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: K.76, T.147, D.150 Ligands: ACT.22 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.147, A:T.147 EDO.2: 1 residues within 4Å: Chain A: K.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.243 EDO.25: 3 residues within 4Å: Chain B: G.98, D.99 Ligands: ACT.38 No protein-ligand interaction detected (PLIP) EDO.26: 2 residues within 4Å: Chain B: Q.50, K.63 No protein-ligand interaction detected (PLIP) EDO.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.28: 3 residues within 4Å: Chain A: N.51, S.164 Chain B: E.195 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.51, A:S.164 EDO.29: 3 residues within 4Å: Chain B: C.45, Q.46, I.47 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.45, B:I.47

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

NA.3: 6 residues within 4Å: Chain A: E.11, G.13, Q.140, S.164, V.165 Ligands: 6DB.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.13, A:Q.140, A:V.165 Water bridges: A:E.166 NA.4: 5 residues within 4Å: Chain A: L.218, R.219, K.220, D.222, K.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.220, A:D.222 NA.5: 4 residues within 4Å: Chain A: N.92, T.144, A.145 Ligands: 6DB.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.92, A:T.144, A:T.144, A:A.145 NA.6: 5 residues within 4Å: Chain A: A.89, G.90, S.207, G.208, G.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.90, A:G.90, A:G.208 NA.7: 3 residues within 4Å: Chain A: D.222, T.223, A.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.222, A:T.223, A:A.224 Water bridges: A:L.225 NA.8: 2 residues within 4Å: Chain A: S.113, S.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.113, A:S.113, A:S.116 NA.9: 1 residues within 4Å: Ligands: ACT.23 No protein-ligand interaction detected (PLIP) NA.30: 5 residues within 4Å: Chain B: G.93, F.94, V.202, G.203, P.204 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.94, B:G.203 Water bridges: B:V.202 NA.31: 5 residues within 4Å: Chain B: V.96, M.97, S.100, L.172, D.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.97, B:S.100, B:D.178

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

CL.10: 3 residues within 4Å: Chain A: C.45, Q.46, I.47 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: G.134, S.156 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: W.17, A.89, G.90, I.91, N.183, V.254 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: K.160, R.176 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: A.184 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: K.25 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: Q.2 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: D.158, R.176 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: G.21, P.22, G.23, K.25 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: S.113, S.116 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: V.252, D.253 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain A: K.193 Chain B: G.12, F.19, S.20 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain B: G.21, P.22, G.23, K.25 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 3 residues within 4Å: Chain A: P.106, G.107, L.108 No protein-ligand interaction detected (PLIP) GOL.36: 6 residues within 4Å: Chain B: E.221, D.222, T.223, A.224, L.225 Ligands: ACT.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.222, B:L.225

2 x 6DB: octopine(Non-covalent)

6DB.21: 19 residues within 4Å: Chain A: E.11, Y.14, N.18, W.52, A.69, A.70, M.71, S.72, R.77, G.90, N.92, Q.140, T.143, T.144, N.183, F.211, V.214 Ligands: NA.3, NA.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.52, A:A.70, A:T.143, A:V.214 Hydrogen bonds: A:N.18, A:A.69, A:A.70, A:S.72, A:S.72, A:S.72, A:S.72, A:N.92, A:Q.140, A:Q.140, A:T.144, A:N.183 Salt bridges: A:E.11, A:R.77 pi-Cation interactions: A:Y.14 6DB.37: 17 residues within 4Å: Chain B: E.11, Y.14, N.18, W.52, A.69, A.70, M.71, S.72, R.77, G.90, N.92, Q.140, T.143, T.144, N.183, F.211, V.214 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.52, B:T.143, B:V.214 Hydrogen bonds: B:Y.14, B:Y.14, B:N.18, B:A.69, B:A.70, B:S.72, B:S.72, B:S.72, B:N.92, B:Q.140, B:Q.140, B:T.144, B:T.144, B:N.183 Salt bridges: B:E.11, B:R.77 pi-Cation interactions: B:Y.14

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.22: 4 residues within 4Å: Chain A: R.77, S.142, T.143 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.77 ACT.23: 2 residues within 4Å: Chain A: K.163 Ligands: NA.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.163 ACT.24: 4 residues within 4Å: Chain A: L.26, I.47, V.48, A.49 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.26 Hydrogen bonds: A:A.49, A:A.49 ACT.38: 4 residues within 4Å: Chain B: K.197, G.198, K.200 Ligands: EDO.25 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.198 Water bridges: B:A.199, B:K.200, B:K.200 Salt bridges: B:K.200 ACT.39: 5 residues within 4Å: Chain B: K.62, R.219, E.221, D.222 Ligands: GOL.36 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.221, B:D.222 Salt bridges: B:K.62, B:R.219 ACT.40: 4 residues within 4Å: Chain B: M.56, R.77, S.142, T.143 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.77 Salt bridges: B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vigouroux, A. et al., Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens. Sci Rep (2017)

Release Date

2017-12-20

Peptides

Octopine-binding periplasmic protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Octopine-binding periplasmic protein

Related Entries With Identical Sequence