SMTL ID : 6ome.2 (1 other biounit)

Crystal structure of a probable cytosol aminopeptidase (Leucine aminopeptidase, LAP) from Chlamydia trachomatis D/UW-3/Cx

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

3 x CO3: CARBONATE ION(Non-functional Binders)

CO3.1: 8 residues within 4Å: Chain A: K.272, A.355, E.356, G.357, R.358, L.383 Ligands: EDO.5, ZN.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.355, A:E.356, A:G.357, A:R.358, A:L.383 CO3.15: 8 residues within 4Å: Chain B: K.272, A.355, E.356, G.357, R.358, L.383 Ligands: EDO.19, ZN.20 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.355, B:E.356, B:G.357, B:R.358, B:L.383 Water bridges: B:K.272 CO3.29: 8 residues within 4Å: Chain C: K.272, A.355, E.356, G.357, R.358, L.383 Ligands: EDO.33, ZN.34 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.355, C:E.356, C:G.357, C:R.358, C:L.383 Water bridges: C:K.272

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

EDO.2: 7 residues within 4Å: Chain A: S.143, R.192, T.416, E.418, P.485, Y.486, R.496 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.143, A:S.143, A:R.192, A:E.418, A:E.418, A:R.496 EDO.4: 2 residues within 4Å: Chain A: D.265, F.505 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.265, A:L.506 EDO.5: 6 residues within 4Å: Chain A: D.354, R.358, L.383, T.384, G.385 Ligands: CO3.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.354, A:R.358, A:G.385 Water bridges: A:R.358, A:A.386 EDO.16: 7 residues within 4Å: Chain B: S.143, R.192, T.416, E.418, P.485, Y.486, R.496 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.143, B:S.143, B:R.192, B:E.418, B:E.418, B:R.496 EDO.18: 2 residues within 4Å: Chain B: D.265, F.505 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.265, B:L.506 EDO.19: 6 residues within 4Å: Chain B: D.354, R.358, L.383, T.384, G.385 Ligands: CO3.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.354, B:R.358, B:G.385 Water bridges: B:R.358, B:A.386 EDO.30: 7 residues within 4Å: Chain C: S.143, R.192, T.416, E.418, P.485, Y.486, R.496 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.143, C:S.143, C:R.192, C:E.418, C:E.418, C:R.496 EDO.32: 2 residues within 4Å: Chain C: D.265, F.505 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.265, C:L.506 EDO.33: 6 residues within 4Å: Chain C: D.354, R.358, L.383, T.384, G.385 Ligands: CO3.29 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.354, C:R.358, C:G.385 Water bridges: C:R.358, C:A.386

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

SO4.3: 8 residues within 4Å: Chain A: G.330, S.331 Chain B: G.330, S.331 Chain C: G.330, S.331 Ligands: SO4.17, SO4.31 8 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:S.331, A:S.331, B:S.331, B:S.331 Water bridges: C:G.330, C:S.331, A:S.331, B:S.331 SO4.17: 8 residues within 4Å: Chain A: G.330, S.331 Chain B: G.330, S.331 Chain C: G.330, S.331 Ligands: SO4.3, SO4.31 8 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:S.331, C:S.331, A:S.331, B:S.331 Water bridges: C:S.331, A:G.330, A:S.331, B:S.331 SO4.31: 8 residues within 4Å: Chain A: G.330, S.331 Chain B: G.330, S.331 Chain C: G.330, S.331 Ligands: SO4.3, SO4.17 8 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:S.331, B:S.331, A:S.331, A:S.331 Water bridges: C:S.331, B:G.330, B:S.331, A:S.331

6 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: K.272, D.277, D.295, E.356 Ligands: CO3.1, ZN.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.277, A:D.295, A:E.356, H2O.5 ZN.7: 4 residues within 4Å: Chain A: D.277, D.354, E.356 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.277, A:D.354, A:D.354, A:E.356, H2O.5 ZN.20: 6 residues within 4Å: Chain B: K.272, D.277, D.295, E.356 Ligands: CO3.15, ZN.21 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.277, B:D.295, B:E.356, H2O.19 ZN.21: 4 residues within 4Å: Chain B: D.277, D.354, E.356 Ligands: ZN.20 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.277, B:D.354, B:D.354, B:E.356, H2O.19 ZN.34: 6 residues within 4Å: Chain C: K.272, D.277, D.295, E.356 Ligands: CO3.29, ZN.35 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.277, C:D.295, C:E.356, H2O.33 ZN.35: 4 residues within 4Å: Chain C: D.277, D.354, E.356 Ligands: ZN.34 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.277, C:D.354, C:D.354, C:E.356, H2O.33

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

NA.8: 1 residues within 4Å: Chain A: E.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.186 NA.9: 4 residues within 4Å: Chain A: A.215, F.218, A.219, L.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.221, A:L.221 NA.10: 3 residues within 4Å: Chain A: D.282 Ligands: CL.12, LEU.14 3 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: L.14, L.14 Water bridges: A:D.282 NA.11: 3 residues within 4Å: Chain A: A.474, G.475, Y.478 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.474, A:Y.478 NA.22: 1 residues within 4Å: Chain B: E.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.186 NA.23: 4 residues within 4Å: Chain B: A.215, F.218, A.219, L.221 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.215, B:L.221 NA.24: 3 residues within 4Å: Chain B: D.282 Ligands: CL.26, LEU.28 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:D.282, L.28 Water bridges: B:D.282 NA.25: 3 residues within 4Å: Chain B: A.474, G.475, Y.478 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.474, B:Y.478 NA.36: 1 residues within 4Å: Chain C: E.186 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.186 NA.37: 4 residues within 4Å: Chain C: A.215, F.218, A.219, L.221 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.215, C:L.221 NA.38: 3 residues within 4Å: Chain C: D.282 Ligands: CL.40, LEU.42 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: L.42, C:D.282 Water bridges: C:D.282 NA.39: 3 residues within 4Å: Chain C: A.474, G.475, Y.478 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.474, C:Y.478

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

CL.12: 5 residues within 4Å: Chain A: D.282 Chain C: P.285, G.286 Ligands: NA.10, LEU.14 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: R.376 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain A: P.285, G.286 Chain B: D.282 Ligands: NA.24, LEU.28 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: R.376 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain B: P.285, G.286 Chain C: D.282 Ligands: NA.38, LEU.42 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain C: R.376 Ligand excluded by PLIP

3 x LEU: LEUCINE(Non-covalent)

LEU.14: 6 residues within 4Å: Chain A: D.282 Chain C: P.285, G.286, K.287 Ligands: NA.10, CL.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.287 Hydrogen bonds: C:G.286, C:K.287 LEU.28: 6 residues within 4Å: Chain A: P.285, G.286, K.287 Chain B: D.282 Ligands: NA.24, CL.26 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:K.287 Hydrogen bonds: A:G.286, A:K.287 LEU.42: 6 residues within 4Å: Chain B: P.285, G.286, K.287 Chain C: D.282 Ligands: NA.38, CL.40 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.287 Hydrogen bonds: B:G.286, B:K.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Crystal structure of a probable cytosol aminopeptidase (Leucine aminopeptidase, LAP) from Chlamydia trachomatis D/UW-3/Cx. To Be Published

Release Date

2019-05-01

Peptides

Probable cytosol aminopeptidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Probable cytosol aminopeptidase

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