SMTL ID : 4ksi.1

Crystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.305, K.312, D.385, E.387 Ligands: MG.2, SO4.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.305, A:D.385, A:D.385, A:E.387, H2O.1 MG.2: 6 residues within 4Å: Chain A: K.300, D.305, D.325, E.387 Ligands: MG.1, SO4.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.305, A:D.325, A:E.387, H2O.1, H2O.10 MG.15: 6 residues within 4Å: Chain B: D.305, K.312, D.385, E.387 Ligands: MG.16, SO4.17 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.305, B:D.385, B:D.385, B:E.387, H2O.19 MG.16: 6 residues within 4Å: Chain B: K.300, D.305, D.325, E.387 Ligands: MG.15, SO4.17 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.305, B:D.325, B:E.387, H2O.19, H2O.28 MG.29: 6 residues within 4Å: Chain C: D.305, K.312, D.385, E.387 Ligands: MG.30, SO4.31 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.305, C:D.385, C:D.385, C:E.387, H2O.37 MG.30: 6 residues within 4Å: Chain C: K.300, D.305, D.325, E.387 Ligands: MG.29, SO4.31 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.305, C:D.325, C:E.387, H2O.37, H2O.46 MG.43: 6 residues within 4Å: Chain D: D.305, K.312, D.385, E.387 Ligands: MG.44, SO4.45 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.305, D:D.385, D:D.385, D:E.387, H2O.55 MG.44: 6 residues within 4Å: Chain D: K.300, D.305, D.325, E.387 Ligands: MG.43, SO4.45 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.305, D:D.325, D:E.387, H2O.55, H2O.64 MG.57: 6 residues within 4Å: Chain E: D.305, K.312, D.385, E.387 Ligands: MG.58, SO4.59 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.305, E:D.385, E:D.385, E:E.387, H2O.73 MG.58: 6 residues within 4Å: Chain E: K.300, D.305, D.325, E.387 Ligands: MG.57, SO4.59 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.305, E:D.325, E:E.387, H2O.73, H2O.82 MG.71: 6 residues within 4Å: Chain F: D.305, K.312, D.385, E.387 Ligands: MG.72, SO4.73 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.305, F:D.385, F:D.385, F:E.387, H2O.91 MG.72: 6 residues within 4Å: Chain F: K.300, D.305, D.325, E.387 Ligands: MG.71, SO4.73 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.305, F:D.325, F:E.387, H2O.91, H2O.101

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

SO4.3: 10 residues within 4Å: Chain A: K.300, D.385, A.386, E.387, G.388, R.389, T.412, L.413 Ligands: MG.1, MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.387, A:G.388, A:R.389, A:L.413 Water bridges: A:K.300, A:K.300 Salt bridges: A:K.300, A:R.389 SO4.14: 6 residues within 4Å: Chain A: A.230, A.233, E.234, K.237, I.251, Y.278 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.237 SO4.17: 10 residues within 4Å: Chain B: K.300, D.385, A.386, E.387, G.388, R.389, T.412, L.413 Ligands: MG.15, MG.16 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.387, B:G.388, B:R.389, B:L.413 Water bridges: B:K.300, B:K.300 Salt bridges: B:K.300, B:R.389 SO4.28: 6 residues within 4Å: Chain B: A.230, A.233, E.234, K.237, I.251, Y.278 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.237 SO4.31: 10 residues within 4Å: Chain C: K.300, D.385, A.386, E.387, G.388, R.389, T.412, L.413 Ligands: MG.29, MG.30 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.387, C:G.388, C:R.389, C:L.413 Water bridges: C:K.300, C:K.300 Salt bridges: C:K.300, C:R.389 SO4.42: 6 residues within 4Å: Chain C: A.230, A.233, E.234, K.237, I.251, Y.278 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.237 SO4.45: 10 residues within 4Å: Chain D: K.300, D.385, A.386, E.387, G.388, R.389, T.412, L.413 Ligands: MG.43, MG.44 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.387, D:G.388, D:R.389, D:L.413 Water bridges: D:K.300, D:K.300 Salt bridges: D:K.300, D:R.389 SO4.56: 6 residues within 4Å: Chain D: A.230, A.233, E.234, K.237, I.251, Y.278 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.234 Salt bridges: D:K.237 SO4.59: 10 residues within 4Å: Chain E: K.300, D.385, A.386, E.387, G.388, R.389, T.412, L.413 Ligands: MG.57, MG.58 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:E.387, E:G.388, E:R.389, E:L.413 Water bridges: E:K.300, E:K.300 Salt bridges: E:K.300, E:R.389 SO4.70: 6 residues within 4Å: Chain E: A.230, A.233, E.234, K.237, I.251, Y.278 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.234 Salt bridges: E:K.237 SO4.73: 10 residues within 4Å: Chain F: K.300, D.385, A.386, E.387, G.388, R.389, T.412, L.413 Ligands: MG.71, MG.72 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:E.387, F:G.388, F:R.389, F:L.413 Water bridges: F:K.300, F:K.300 Salt bridges: F:K.300, F:R.389 SO4.84: 6 residues within 4Å: Chain F: A.230, A.233, E.234, K.237, I.251, Y.278 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.234 Salt bridges: F:K.237

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

CL.4: 1 residues within 4Å: Chain A: E.235 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.100, G.103 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: E.235 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: R.100, G.103 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Chain C: E.235 Ligand excluded by PLIP CL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain C: R.100, G.103 Ligand excluded by PLIP CL.46: 1 residues within 4Å: Chain D: E.235 Ligand excluded by PLIP CL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain D: R.100, G.103 Ligand excluded by PLIP CL.60: 1 residues within 4Å: Chain E: E.235 Ligand excluded by PLIP CL.61: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.62: 2 residues within 4Å: Chain E: R.100, G.103 Ligand excluded by PLIP CL.74: 1 residues within 4Å: Chain F: E.235 Ligand excluded by PLIP CL.75: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.76: 2 residues within 4Å: Chain F: R.100, G.103 Ligand excluded by PLIP

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: W.42, Q.43, G.44, D.45, L.46, L.47, G.103, G.104, R.105 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: S.248, V.249, N.250, H.281, C.283 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: N.432, D.433, D.434, L.435, Q.496 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: A.315, E.320 Chain B: N.382, N.383 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: P.28, K.29, I.30, I.32, V.167, E.207 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain B: W.42, Q.43, G.44, D.45, L.46, L.47, G.103, G.104, R.105 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: S.248, V.249, N.250, H.281, C.283 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: N.432, D.433, D.434, L.435, Q.496 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain B: A.315, E.320 Chain C: N.382, N.383 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: P.28, K.29, I.30, I.32, V.167, E.207 Ligand excluded by PLIP GOL.35: 9 residues within 4Å: Chain C: W.42, Q.43, G.44, D.45, L.46, L.47, G.103, G.104, R.105 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain C: S.248, V.249, N.250, H.281, C.283 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain C: N.432, D.433, D.434, L.435, Q.496 Ligand excluded by PLIP GOL.38: 4 residues within 4Å: Chain A: N.382, N.383 Chain C: A.315, E.320 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain C: P.28, K.29, I.30, I.32, V.167, E.207 Ligand excluded by PLIP GOL.49: 9 residues within 4Å: Chain D: W.42, Q.43, G.44, D.45, L.46, L.47, G.103, G.104, R.105 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain D: S.248, V.249, N.250, H.281, C.283 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain D: N.432, D.433, D.434, L.435, Q.496 Ligand excluded by PLIP GOL.52: 4 residues within 4Å: Chain D: A.315, E.320 Chain E: N.382, N.383 Ligand excluded by PLIP GOL.53: 6 residues within 4Å: Chain D: P.28, K.29, I.30, I.32, V.167, E.207 Ligand excluded by PLIP GOL.63: 9 residues within 4Å: Chain E: W.42, Q.43, G.44, D.45, L.46, L.47, G.103, G.104, R.105 Ligand excluded by PLIP GOL.64: 5 residues within 4Å: Chain E: S.248, V.249, N.250, H.281, C.283 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain E: N.432, D.433, D.434, L.435, Q.496 Ligand excluded by PLIP GOL.66: 4 residues within 4Å: Chain E: A.315, E.320 Chain F: N.382, N.383 Ligand excluded by PLIP GOL.67: 6 residues within 4Å: Chain E: P.28, K.29, I.30, I.32, V.167, E.207 Ligand excluded by PLIP GOL.77: 9 residues within 4Å: Chain F: W.42, Q.43, G.44, D.45, L.46, L.47, G.103, G.104, R.105 Ligand excluded by PLIP GOL.78: 5 residues within 4Å: Chain F: S.248, V.249, N.250, H.281, C.283 Ligand excluded by PLIP GOL.79: 5 residues within 4Å: Chain F: N.432, D.433, D.434, L.435, Q.496 Ligand excluded by PLIP GOL.80: 4 residues within 4Å: Chain D: N.382, N.383 Chain F: A.315, E.320 Ligand excluded by PLIP GOL.81: 6 residues within 4Å: Chain F: P.28, K.29, I.30, I.32, V.167, E.207 Ligand excluded by PLIP

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.12: 4 residues within 4Å: Chain A: W.460, M.463, K.464, D.469 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.469 IMD.26: 4 residues within 4Å: Chain B: W.460, M.463, K.464, D.469 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.469 IMD.40: 4 residues within 4Å: Chain C: W.460, M.463, K.464, D.469 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.469 IMD.54: 4 residues within 4Å: Chain D: W.460, M.463, K.464, D.469 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.469 IMD.68: 4 residues within 4Å: Chain E: W.460, M.463, K.464, D.469 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.469 IMD.82: 4 residues within 4Å: Chain F: W.460, M.463, K.464, D.469 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.469

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.13: 9 residues within 4Å: Chain A: P.118, H.122, N.157, S.160, A.161, T.164, A.445, S.446, S.520 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.118, A:A.161 Hydrogen bonds: A:S.160, A:T.164 MPD.27: 9 residues within 4Å: Chain B: P.118, H.122, N.157, S.160, A.161, T.164, A.445, S.446, S.520 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.118, B:A.161 Hydrogen bonds: B:S.160, B:T.164 MPD.41: 9 residues within 4Å: Chain C: P.118, H.122, N.157, S.160, A.161, T.164, A.445, S.446, S.520 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.118, C:A.161 Hydrogen bonds: C:S.160, C:T.164 MPD.55: 9 residues within 4Å: Chain D: P.118, H.122, N.157, S.160, A.161, T.164, A.445, S.446, S.520 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:P.118, D:A.161 Hydrogen bonds: D:S.160, D:T.164, D:T.164 MPD.69: 9 residues within 4Å: Chain E: P.118, H.122, N.157, S.160, A.161, T.164, A.445, S.446, S.520 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:P.118, E:A.161 Hydrogen bonds: E:S.160, E:T.164, E:T.164 MPD.83: 9 residues within 4Å: Chain F: P.118, H.122, N.157, S.160, A.161, T.164, A.445, S.446, S.520 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:P.118, F:A.161 Hydrogen bonds: F:S.160, F:T.164, F:T.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duprez, K. et al., Structure of tomato wound-induced leucine aminopeptidase sheds light on substrate specificity. Acta Crystallogr.,Sect.D (2014)

Release Date

2013-06-12

Peptides

Leucine aminopeptidase 1, chloroplastic: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Leucine aminopeptidase 1, chloroplastic