SMTL ID : 5d8g.1

A structural view on the dissociation of E. coli Tryptophanase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: A.61, R.65 Chain D: A.61, R.65 Ligands: CL.22 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: A.61, R.65 Chain C: A.61, R.65 Ligands: CL.15 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: A.61, R.65 Chain C: A.61, R.65 Ligands: CL.8 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain A: A.61, R.65 Chain D: A.61, R.65 Ligands: CL.1 Ligand excluded by PLIP

12 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: Q.115, E.289 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.289, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain A: D.49, R.330, H.354, T.417, I.418 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.354, H2O.11 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: Q.115, E.289 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.289, H2O.17, H2O.18 MG.12: 5 residues within 4Å: Chain B: D.49, R.330, H.354, T.417, I.418 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.354, H2O.28 MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain C: Q.115, E.289 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.289, H2O.33, H2O.34 MG.19: 5 residues within 4Å: Chain C: D.49, R.330, H.354, T.417, I.418 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.354, H2O.44 MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain D: Q.115, E.289 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.289, H2O.50, H2O.50 MG.26: 5 residues within 4Å: Chain D: D.49, R.330, H.354, T.417, I.418 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.354, H2O.60

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 9 residues within 4Å: Chain A: L.47, T.48, D.133, V.390, I.392, L.396, R.415 Chain B: Y.70, Y.303 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.415, A:R.415 Water bridges: A:T.48, B:G.304 Salt bridges: A:R.415 EPE.10: 9 residues within 4Å: Chain A: Y.70, Y.303 Chain B: L.47, T.48, D.133, V.390, I.392, L.396, R.415 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.415, B:R.415 Water bridges: B:T.48, A:G.304 Salt bridges: B:R.415 EPE.17: 9 residues within 4Å: Chain C: L.47, T.48, D.133, V.390, I.392, L.396, R.415 Chain D: Y.70, Y.303 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Water bridges: D:G.304 Hydrogen bonds: C:T.48, C:D.133, C:R.415, C:R.415 Salt bridges: C:R.415 EPE.24: 9 residues within 4Å: Chain C: Y.70, Y.303 Chain D: L.47, T.48, D.133, V.390, I.392, L.396, R.415 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.48, D:D.133, D:R.415, D:R.415 Salt bridges: D:R.415 Water bridges: C:G.304

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

NA.6: 1 residues within 4Å: Chain A: E.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.247 Water bridges: A:T.245 NA.13: 1 residues within 4Å: Chain B: E.247 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.245 NA.20: 1 residues within 4Å: Chain C: E.247 No protein-ligand interaction detected (PLIP) NA.27: 1 residues within 4Å: Chain D: E.247 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.247

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: R.65, E.312, A.315, V.316 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.312, A:E.312, H2O.16 CA.14: 4 residues within 4Å: Chain B: R.65, E.312, A.315, V.316 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.312, B:E.312, H2O.32 CA.21: 4 residues within 4Å: Chain C: R.65, E.312, A.315, V.316 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.312, C:E.312, H2O.48 CA.28: 4 residues within 4Å: Chain D: R.65, E.312, A.315, V.316 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.312, D:E.312, H2O.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Green, K. et al., A structural view of the dissociation of Escherichia coli tryptophanase. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-12-09

Peptides

Tryptophanase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Tryptophanase