- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 12 x ZN: ZINC ION(Non-covalent)
ZN.2: 9 residues within 4Å:- Chain A: D.296, G.298, K.303, N.349, D.376, E.378
- Ligands: CO3.1, ZN.3, 1PE.6
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.296, A:D.376, A:D.376, A:E.378
ZN.3: 8 residues within 4Å:- Chain A: K.291, I.293, D.296, D.316, E.378
- Ligands: CO3.1, ZN.2, 1PE.6
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.296, A:D.316, A:E.378
ZN.9: 6 residues within 4Å:- Chain B: K.291, I.293, D.296, D.316, E.378
- Ligands: ZN.10
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.296, B:D.316, B:E.378, H2O.5
ZN.10: 7 residues within 4Å:- Chain B: D.296, G.298, K.303, N.349, D.376, E.378
- Ligands: ZN.9
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.296, B:D.376, B:D.376, B:E.378
ZN.14: 7 residues within 4Å:- Chain C: D.296, G.298, K.303, N.349, D.376, E.378
- Ligands: ZN.15
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.296, C:D.296, C:D.376, C:D.376, C:E.378
ZN.15: 7 residues within 4Å:- Chain C: K.291, I.293, D.296, D.316, E.378
- Ligands: ZN.14, CO3.16
3 PLIP interactions:3 interactions with chain C- Metal complexes: C:D.296, C:D.316, C:E.378
ZN.19: 7 residues within 4Å:- Chain D: D.296, G.298, K.303, N.349, D.376, E.378
- Ligands: ZN.20
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.296, D:D.376, D:D.376, D:E.378
ZN.20: 7 residues within 4Å:- Chain D: K.291, I.293, D.296, D.316, E.378
- Ligands: ZN.19, CO3.21
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.296, D:D.316, D:E.378
ZN.24: 5 residues within 4Å:- Chain E: D.296, K.303, D.376, E.378
- Ligands: ZN.25
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:D.296, E:D.376, E:D.376, E:E.378
ZN.25: 8 residues within 4Å:- Chain E: K.291, I.293, D.296, D.316, E.378
- Ligands: ZN.24, CO3.26, 1PE.27
3 PLIP interactions:3 interactions with chain E- Metal complexes: E:D.296, E:D.316, E:E.378
ZN.31: 7 residues within 4Å:- Chain F: K.291, D.296, K.303, N.349, D.376, E.378
- Ligands: ZN.32
5 PLIP interactions:5 interactions with chain F- Metal complexes: F:D.296, F:D.296, F:D.376, F:D.376, F:E.378
ZN.32: 6 residues within 4Å:- Chain F: K.291, D.296, D.316, E.378
- Ligands: ZN.31, CO3.33
3 PLIP interactions:3 interactions with chain F- Metal complexes: F:D.296, F:D.316, F:E.378
- 9 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 7 residues within 4Å:- Chain A: E.42, G.43, K.135, L.136, S.137, K.138
- Chain D: K.81
5 PLIP interactions:4 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:G.43, A:S.137, A:S.137, A:S.137
- Salt bridges: D:K.81
SO4.8: 5 residues within 4Å:- Chain A: I.18, E.19, Y.20, N.21
- Ligands: 1PE.5
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.20, A:N.21
SO4.13: 5 residues within 4Å:- Chain B: P.306, G.307, S.308, M.309, I.310
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:G.307, B:S.308, B:M.309
SO4.17: 6 residues within 4Å:- Chain A: S.352, K.353
- Chain B: S.352, K.353
- Chain C: S.352, K.353
11 PLIP interactions:3 interactions with chain A, 4 interactions with chain C, 4 interactions with chain B- Hydrogen bonds: A:S.352, A:K.353, C:S.352, C:S.352, C:K.353, B:S.352, B:S.352, B:K.353
- Salt bridges: A:K.353, C:K.353, B:K.353
SO4.18: 6 residues within 4Å:- Chain C: A.305, P.306, G.307, S.308, M.309, I.310
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:G.307, C:S.308, C:M.309
- Water bridges: C:S.308, C:I.310
SO4.23: 6 residues within 4Å:- Chain D: S.352, K.353
- Chain E: S.352, K.353
- Chain F: S.352, K.353
9 PLIP interactions:4 interactions with chain D, 3 interactions with chain F, 2 interactions with chain E- Hydrogen bonds: D:S.352, D:S.352, D:K.353, F:S.352, F:K.353, E:S.352, E:K.353
- Salt bridges: D:K.353, F:K.353
SO4.29: 5 residues within 4Å:- Chain E: I.18, E.19, Y.20, N.21
- Ligands: 1PE.28
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Y.20, E:N.21
SO4.30: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)SO4.34: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)- 8 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.5: 5 residues within 4Å:- Chain A: Y.20, E.233, Q.236, K.237
- Ligands: SO4.8
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.237
1PE.6: 18 residues within 4Å:- Chain A: K.291, D.296, K.303, G.307, S.308, M.309, M.313, F.315, D.316, T.403, L.404, T.405, G.406, L.409, Y.410, A.494
- Ligands: ZN.2, ZN.3
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.303
1PE.7: 7 residues within 4Å:- Chain A: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328
1 PLIP interactions:1 interactions with chain A- Water bridges: A:K.237
1PE.12: 7 residues within 4Å:- Chain B: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328
No protein-ligand interaction detected (PLIP)1PE.22: 7 residues within 4Å:- Chain D: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:N.21
1PE.27: 14 residues within 4Å:- Chain E: K.303, G.307, S.308, M.309, M.313, F.315, D.316, T.403, L.404, T.405, G.406, L.409, A.494
- Ligands: ZN.25
1 PLIP interactions:1 interactions with chain E- Water bridges: E:K.303
1PE.28: 5 residues within 4Å:- Chain E: Y.20, E.233, Q.236, K.237
- Ligands: SO4.29
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:K.237
1PE.35: 7 residues within 4Å:- Chain D: S.171, T.172
- Chain F: N.366, K.368, T.369, D.460, E.481
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:K.368
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- de Koning-Ward, T.F. et al., Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties. Mbio (2024)
- Release Date
- 2024-04-24
- Peptides
- Leucine aminopeptidase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
HC
ID
JE
KF
L
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 12 x ZN: ZINC ION(Non-covalent)
- 9 x SO4: SULFATE ION(Non-functional Binders)
- 8 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- de Koning-Ward, T.F. et al., Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties. Mbio (2024)
- Release Date
- 2024-04-24
- Peptides
- Leucine aminopeptidase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
HC
ID
JE
KF
L