- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 12 x ZN: ZINC ION(Non-covalent)
ZN.2: 7 residues within 4Å:- Chain A: K.291, D.296, D.316, E.378, T.403
- Ligands: ZN.3, WRC.4
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.296, A:D.316, A:E.378
ZN.3: 6 residues within 4Å:- Chain A: D.296, K.303, D.376, E.378
- Ligands: ZN.2, WRC.4
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Ligand interactions- Metal complexes: A:D.296, A:D.376, A:D.376, A:E.378, WRC.4
ZN.11: 6 residues within 4Å:- Chain B: K.291, D.296, D.316, E.378
- Ligands: ZN.12, WRC.13
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.296, B:D.316, B:E.378
ZN.12: 6 residues within 4Å:- Chain B: D.296, K.303, D.376, E.378
- Ligands: ZN.11, WRC.13
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Ligand interactions- Metal complexes: B:D.296, B:D.376, B:D.376, B:E.378, WRC.13
ZN.17: 6 residues within 4Å:- Chain C: K.291, D.296, D.316, E.378
- Ligands: ZN.18, WRC.19
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.296, C:D.316, C:D.316, C:E.378
ZN.18: 6 residues within 4Å:- Chain C: D.296, K.303, D.376, E.378
- Ligands: ZN.17, WRC.19
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Ligand interactions- Metal complexes: C:D.296, C:D.376, C:D.376, C:E.378, WRC.19
ZN.24: 6 residues within 4Å:- Chain D: K.291, D.296, D.316, E.378
- Ligands: ZN.25, WRC.26
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.296, D:D.316, D:E.378
ZN.25: 6 residues within 4Å:- Chain D: D.296, K.303, D.376, E.378
- Ligands: ZN.24, WRC.26
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Ligand interactions- Metal complexes: D:D.296, D:D.376, D:D.376, D:E.378, WRC.26
ZN.31: 7 residues within 4Å:- Chain E: K.291, D.296, D.316, E.378, T.403
- Ligands: ZN.32, WRC.33
2 PLIP interactions:2 interactions with chain E- Metal complexes: E:D.316, E:E.378
ZN.32: 6 residues within 4Å:- Chain E: D.296, D.376, A.377, E.378
- Ligands: ZN.31, WRC.33
5 PLIP interactions:4 interactions with chain E, 1 Ligand-Ligand interactions- Metal complexes: E:D.296, E:D.376, E:D.376, E:E.378, WRC.33
ZN.37: 6 residues within 4Å:- Chain F: D.296, K.303, D.376, E.378
- Ligands: ZN.38, WRC.39
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.38: 7 residues within 4Å:- Chain F: K.291, D.296, D.316, E.378
- Ligands: CO3.36, ZN.37, WRC.39
4 PLIP interactions:3 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:D.316, F:D.316, F:E.378, H2O.52
- 6 x WRC: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide
WRC.4: 18 residues within 4Å:- Chain A: K.291, D.296, K.303, G.307, M.309, F.315, N.374, D.376, E.378, L.404, T.405, G.406, L.409, A.494, F.500
- Ligands: CO3.1, ZN.2, ZN.3
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:F.315
- Hydrogen bonds: A:K.303, A:L.404, A:G.406
- Water bridges: A:K.303, A:A.407
WRC.13: 21 residues within 4Å:- Chain B: K.291, D.296, K.303, G.307, M.309, F.315, D.316, D.376, A.377, E.378, R.380, L.404, T.405, G.406, L.409, S.471, A.494, F.500
- Ligands: CO3.10, ZN.11, ZN.12
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:F.315, B:A.377
- Hydrogen bonds: B:K.303, B:G.406, B:S.471
- Water bridges: B:D.376
WRC.19: 21 residues within 4Å:- Chain C: K.291, D.296, K.303, G.307, S.308, M.309, D.316, N.374, D.376, E.378, R.380, L.404, T.405, G.406, L.409, S.471, A.494, F.500
- Ligands: CO3.16, ZN.17, ZN.18
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:K.291, C:K.303, C:G.406
- Water bridges: C:K.303
- Halogen bonds: C:G.307
WRC.26: 18 residues within 4Å:- Chain D: K.291, D.296, K.303, G.307, M.309, F.315, D.376, E.378, R.380, L.404, T.405, G.406, L.409, A.494, F.500
- Ligands: CO3.23, ZN.24, ZN.25
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:F.315, D:A.494
- Hydrogen bonds: D:K.303, D:L.404, D:G.406
- Water bridges: D:K.303, D:D.376
- Halogen bonds: D:G.307
WRC.33: 18 residues within 4Å:- Chain E: K.291, D.296, K.303, G.307, M.309, D.316, N.374, D.376, E.378, L.404, T.405, G.406, L.409, A.494, F.500
- Ligands: CO3.30, ZN.31, ZN.32
5 PLIP interactions:5 interactions with chain E- Hydrophobic interactions: E:L.409
- Hydrogen bonds: E:K.303, E:D.376, E:G.406
- Halogen bonds: E:G.307
WRC.39: 21 residues within 4Å:- Chain F: K.291, D.296, K.303, G.307, M.309, L.312, F.315, N.374, D.376, A.377, E.378, R.380, L.404, T.405, G.406, L.409, A.494, F.500
- Ligands: CO3.36, ZN.37, ZN.38
9 PLIP interactions:9 interactions with chain F- Hydrophobic interactions: F:A.377
- Hydrogen bonds: F:K.303, F:L.404, F:G.406
- Water bridges: F:D.296, F:D.296, F:K.303, F:D.376
- Halogen bonds: F:G.307
- 13 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.5: 6 residues within 4Å:- Chain A: Y.20, N.21, H.25, F.206, K.237, Y.328
2 PLIP interactions:2 interactions with chain A- Water bridges: A:Y.328, A:Y.328
1PE.6: 5 residues within 4Å:- Chain A: Y.20, N.21, E.233, K.237
- Ligands: SO4.7
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.21, A:K.237
1PE.14: 6 residues within 4Å:- Chain B: Y.20, H.25, F.206, K.237, L.238, Y.328
No protein-ligand interaction detected (PLIP)1PE.15: 3 residues within 4Å:- Chain B: Y.20, E.233, K.237
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.237
1PE.20: 4 residues within 4Å:- Chain C: Y.20, E.233, K.237
- Ligands: 1PE.21
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:K.237
- Hydrogen bonds: C:K.237
1PE.21: 7 residues within 4Å:- Chain C: Y.20, N.21, H.25, F.206, K.237, Y.328
- Ligands: 1PE.20
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.237, C:Y.328
1PE.22: 6 residues within 4Å:- Chain C: Y.32, G.36, G.37, N.39, N.66, Y.187
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:Y.32
- Hydrogen bonds: C:N.39, C:N.66, C:Y.187
1PE.27: 6 residues within 4Å:- Chain D: Y.20, N.21, H.25, F.206, K.237, Y.328
No protein-ligand interaction detected (PLIP)1PE.28: 4 residues within 4Å:- Chain D: Y.20, N.21, E.233, K.237
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:K.237
- Hydrogen bonds: D:K.237
1PE.34: 6 residues within 4Å:- Chain E: Y.20, N.21, H.25, F.206, K.237, Y.328
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:N.21
1PE.40: 6 residues within 4Å:- Chain F: Y.20, H.25, F.206, K.237, L.238, Y.328
2 PLIP interactions:2 interactions with chain F- Water bridges: F:Y.20, F:N.21
1PE.41: 3 residues within 4Å:- Chain F: E.233, Q.236, K.237
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:K.237
1PE.42: 6 residues within 4Å:- Chain D: S.171, T.172
- Chain F: N.366, K.368, D.460, Q.484
4 PLIP interactions:1 interactions with chain D, 3 interactions with chain F- Hydrogen bonds: D:S.171, F:K.368, F:Q.484
- Water bridges: F:K.368
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 5 residues within 4Å:- Chain A: I.18, E.19, Y.20, N.21
- Ligands: 1PE.6
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:I.18, A:Y.20, A:N.21, A:N.21
SO4.8: 7 residues within 4Å:- Chain A: F.73, N.78, K.81
- Chain D: Y.93, M.94, F.95, S.101
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain D- Hydrogen bonds: A:F.73, D:S.101, D:S.101
- Salt bridges: A:K.81
SO4.9: 6 residues within 4Å:- Chain A: S.352, K.353
- Chain B: S.352, K.353
- Chain C: S.352, K.353
8 PLIP interactions:3 interactions with chain C, 3 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: C:S.352, C:K.353, B:S.352, B:K.353, A:K.353
- Salt bridges: C:K.353, B:K.353, A:K.353
SO4.29: 6 residues within 4Å:- Chain D: S.352, K.353
- Chain E: S.352, K.353
- Chain F: S.352, K.353
6 PLIP interactions:2 interactions with chain E, 2 interactions with chain D, 2 interactions with chain F- Hydrogen bonds: E:K.353, D:K.353, F:K.353
- Salt bridges: E:K.353, D:K.353, F:K.353
SO4.35: 4 residues within 4Å:- Chain E: I.18, E.19, Y.20, N.21
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Y.20, E:N.21
SO4.43: 5 residues within 4Å:- Chain F: N.422, N.423, N.485, T.486, A.487
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:N.422, F:N.423, F:N.485
- 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 2.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x WRC: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide
- 13 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 6 x SO4: SULFATE ION(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