SMTL ID : 5ntg.1

Structure of Leucyl aminopeptidase from Trypanosoma cruzi in complex with citrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-hexamer

Ligands

9 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 14 residues within 4Å: Chain A: K.287, D.292, K.299, M.307, D.310, D.369, E.371, T.399, L.400, T.401, G.402, A.495 Ligands: MN.2, SO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.299, A:D.310, A:L.400, A:G.402 Salt bridges: A:K.287, A:K.299, A:K.299 CIT.4: 9 residues within 4Å: Chain A: R.112, T.113, E.423, L.424, L.427, F.438 Chain B: E.420, E.423, P.439 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.439, A:F.438 Hydrogen bonds: B:E.420, B:E.423, B:E.423, A:E.423 Salt bridges: A:R.112 CIT.5: 14 residues within 4Å: Chain B: K.287, D.292, K.299, M.307, D.310, D.369, E.371, T.399, L.400, T.401, G.402, A.495 Ligands: MN.6, SO4.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.400, B:G.402 Water bridges: B:A.495 Salt bridges: B:K.287, B:K.299, B:K.299 CIT.8: 14 residues within 4Å: Chain C: K.287, D.292, K.299, M.307, D.310, D.369, E.371, T.399, L.400, T.401, G.402, A.495 Ligands: MN.9, SO4.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.299, C:D.310, C:L.400, C:G.402 Salt bridges: C:K.287, C:K.299, C:K.299 CIT.11: 9 residues within 4Å: Chain C: R.112, T.113, E.423, L.424, L.427, F.438 Chain D: E.420, E.423, P.439 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.438, D:P.439 Hydrogen bonds: C:E.423, D:E.420, D:E.423, D:E.423 Salt bridges: C:R.112 CIT.12: 14 residues within 4Å: Chain D: K.287, D.292, K.299, M.307, D.310, D.369, E.371, T.399, L.400, T.401, G.402, A.495 Ligands: MN.13, SO4.14 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:L.400, D:G.402 Water bridges: D:A.495 Salt bridges: D:K.287, D:K.299, D:K.299 CIT.15: 14 residues within 4Å: Chain E: K.287, D.292, K.299, M.307, D.310, D.369, E.371, T.399, L.400, T.401, G.402, A.495 Ligands: MN.16, SO4.17 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:K.299, E:D.310, E:L.400, E:G.402 Salt bridges: E:K.287, E:K.299, E:K.299 CIT.18: 9 residues within 4Å: Chain E: R.112, T.113, E.423, L.424, L.427, F.438 Chain F: E.420, E.423, P.439 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:F.438, F:P.439 Hydrogen bonds: E:E.423, F:E.420, F:E.423, F:E.423 Salt bridges: E:R.112 CIT.19: 14 residues within 4Å: Chain F: K.287, D.292, K.299, M.307, D.310, D.369, E.371, T.399, L.400, T.401, G.402, A.495 Ligands: MN.20, SO4.21 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:L.400, F:G.402 Water bridges: F:A.495 Salt bridges: F:K.287, F:K.299, F:K.299

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: D.292, K.299, D.369, E.371 Ligands: CIT.1, SO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.292, A:D.369, A:D.369, A:E.371 MN.6: 6 residues within 4Å: Chain B: D.292, K.299, D.369, E.371 Ligands: CIT.5, SO4.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.292, B:D.369, B:D.369, B:E.371 MN.9: 6 residues within 4Å: Chain C: D.292, K.299, D.369, E.371 Ligands: CIT.8, SO4.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.292, C:D.369, C:D.369, C:E.371 MN.13: 6 residues within 4Å: Chain D: D.292, K.299, D.369, E.371 Ligands: CIT.12, SO4.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.292, D:D.369, D:D.369, D:E.371 MN.16: 6 residues within 4Å: Chain E: D.292, K.299, D.369, E.371 Ligands: CIT.15, SO4.17 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.292, E:D.369, E:D.369, E:E.371 MN.20: 6 residues within 4Å: Chain F: D.292, K.299, D.369, E.371 Ligands: CIT.19, SO4.21 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.292, F:D.369, F:D.369, F:E.371

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

SO4.3: 9 residues within 4Å: Chain A: K.287, D.369, A.370, E.371, G.372, R.373, L.400 Ligands: CIT.1, MN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.371, A:G.372, A:R.373 Salt bridges: A:K.287, A:R.373 SO4.7: 9 residues within 4Å: Chain B: K.287, D.369, A.370, E.371, G.372, R.373, L.400 Ligands: CIT.5, MN.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.370, B:E.371, B:G.372, B:R.373, B:L.400 Salt bridges: B:K.287, B:R.373 SO4.10: 9 residues within 4Å: Chain C: K.287, D.369, A.370, E.371, G.372, R.373, L.400 Ligands: CIT.8, MN.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.371, C:G.372, C:R.373 Salt bridges: C:K.287, C:R.373 SO4.14: 9 residues within 4Å: Chain D: K.287, D.369, A.370, E.371, G.372, R.373, L.400 Ligands: CIT.12, MN.13 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:A.370, D:E.371, D:G.372, D:R.373, D:L.400 Salt bridges: D:K.287, D:R.373 SO4.17: 9 residues within 4Å: Chain E: K.287, D.369, A.370, E.371, G.372, R.373, L.400 Ligands: CIT.15, MN.16 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.371, E:G.372, E:R.373 Salt bridges: E:K.287, E:R.373 SO4.21: 9 residues within 4Å: Chain F: K.287, D.369, A.370, E.371, G.372, R.373, L.400 Ligands: CIT.19, MN.20 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:A.370, F:E.371, F:G.372, F:R.373, F:L.400 Salt bridges: F:K.287, F:R.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timm, J. et al., Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation inTrypanosoma brucei. mSphere (2017)

Release Date

2017-08-02

Peptides

Aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Aminopeptidase

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