- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x CO3: CARBONATE ION(Non-functional Binders)
CO3.2: 8 residues within 4Å:- Chain A: K.291, A.377, E.378, G.379, R.380, L.404
- Ligands: ZN.1, 1OT.4
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.378, A:G.379, A:R.380, A:R.380, A:R.380
CO3.12: 8 residues within 4Å:- Chain B: K.291, A.377, E.378, G.379, R.380, L.404
- Ligands: ZN.11, 1OT.14
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.378, B:G.379, B:R.380, B:R.380, B:R.380
CO3.19: 8 residues within 4Å:- Chain C: K.291, A.377, E.378, G.379, R.380, L.404
- Ligands: ZN.18, 1OT.21
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:G.379, C:R.380, C:L.404
CO3.28: 9 residues within 4Å:- Chain D: K.291, D.376, A.377, E.378, G.379, R.380, L.404
- Ligands: ZN.27, 1OT.30
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:G.379, D:R.380, D:L.404
CO3.40: 9 residues within 4Å:- Chain E: K.291, D.376, A.377, E.378, G.379, R.380, L.404
- Ligands: ZN.39, 1OT.42
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:E.378, E:G.379, E:R.380, E:R.380, E:R.380
CO3.50: 9 residues within 4Å:- Chain F: K.291, D.376, A.377, E.378, G.379, R.380, L.404
- Ligands: ZN.49, 1OT.52
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:K.291, F:G.379, F:R.380, F:L.404
- 6 x 1OT: {(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid(Non-covalent)
1OT.4: 17 residues within 4Å:- Chain A: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494
- Ligands: ZN.1, CO3.2, ZN.3
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:F.315, A:L.409, A:A.494
- Hydrogen bonds: A:K.303, A:D.316
- Water bridges: A:R.380
1OT.14: 17 residues within 4Å:- Chain B: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494
- Ligands: ZN.11, CO3.12, ZN.13
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:F.315, B:L.409, B:A.494
- Hydrogen bonds: B:K.291, B:K.303, B:D.316, B:D.376
- Water bridges: B:R.380
1OT.21: 18 residues within 4Å:- Chain C: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494
- Ligands: ZN.18, CO3.19, ZN.20, 1PE.25
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:F.315, C:L.409, C:A.494
- Hydrogen bonds: C:K.291, C:K.303, C:D.316, C:D.376
- Water bridges: C:R.380
1OT.30: 17 residues within 4Å:- Chain D: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, L.409, A.494, F.500
- Ligands: ZN.27, CO3.28, ZN.29
9 PLIP interactions:9 interactions with chain D- Hydrophobic interactions: D:F.315, D:L.409, D:A.494, D:F.500
- Hydrogen bonds: D:K.303, D:D.316, D:D.376, D:D.376
- Water bridges: D:R.380
1OT.42: 17 residues within 4Å:- Chain E: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494
- Ligands: ZN.39, CO3.40, ZN.41
8 PLIP interactions:8 interactions with chain E- Hydrophobic interactions: E:F.315, E:L.409, E:A.494
- Hydrogen bonds: E:K.291, E:K.303, E:D.376
- Water bridges: E:R.380, E:G.406
1OT.52: 17 residues within 4Å:- Chain F: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494
- Ligands: ZN.49, CO3.50, ZN.51
7 PLIP interactions:7 interactions with chain F- Hydrophobic interactions: F:F.315, F:L.409, F:A.494
- Hydrogen bonds: F:K.303, F:D.316, F:D.376, F:D.376
- 11 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 6 residues within 4Å:- Chain A: S.352, K.353
- Chain B: S.352, K.353
- Chain C: S.352, K.353
6 PLIP interactions:2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: A:K.353, C:K.353, B:K.353
- Salt bridges: A:K.353, C:K.353, B:K.353
SO4.6: 5 residues within 4Å:- Chain A: I.18, E.19, Y.20, N.21
- Ligands: 1PE.10
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.20, A:N.21, A:N.21
SO4.7: 8 residues within 4Å:- Chain A: F.73, N.78, K.81, F.82
- Chain D: Y.93, M.94, F.95, S.101
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain D- Salt bridges: A:K.81
- Hydrogen bonds: D:S.101, D:S.101
SO4.8: 4 residues within 4Å:- Chain A: E.42, G.43, L.136, S.137
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain D- Hydrogen bonds: A:G.43, A:S.137
- Water bridges: A:G.43, D:K.81
- Salt bridges: D:K.81
SO4.15: 4 residues within 4Å:- Chain B: E.42, G.43, L.136, S.137
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:G.43, B:S.137, B:K.138
SO4.22: 4 residues within 4Å:- Chain C: E.19, Y.20, N.21
- Ligands: 1PE.23
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Y.20, C:N.21, C:N.21
SO4.31: 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
SO4.32: 4 residues within 4Å:- Chain D: E.19, Y.20, N.21
- Ligands: 2PE.36
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:Y.20, D:N.21, D:N.21
SO4.43: 4 residues within 4Å:- Chain E: I.18, E.19, Y.20, N.21
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:I.18, E:Y.20, E:N.21
SO4.44: 8 residues within 4Å:- Chain C: F.73, N.78, K.81, F.82
- Chain E: Y.93, M.94, F.95, S.101
1 PLIP interactions:1 interactions with chain C- Salt bridges: C:K.81
SO4.53: 4 residues within 4Å:- Chain F: E.19, Y.20, N.21
- Ligands: 1PE.55
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:Y.20, F:N.21, F:N.21
- 15 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.9: 6 residues within 4Å:- Chain A: Y.20, N.21, H.25, F.206, K.237, Y.328
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.237
1PE.10: 5 residues within 4Å:- Chain A: Y.20, E.233, Q.236, K.237
- Ligands: SO4.6
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.237
1PE.23: 4 residues within 4Å:- Chain C: Y.20, E.233, K.237
- Ligands: SO4.22
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:K.237
- Hydrogen bonds: C:K.237
1PE.24: 5 residues within 4Å:- Chain C: Y.20, N.21, H.25, F.206, Y.328
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Y.328
1PE.25: 3 residues within 4Å:- Chain C: N.374, D.376
- Ligands: 1OT.21
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.303
- Water bridges: C:R.380
1PE.33: 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.34: 1 residues within 4Å:- Chain D: K.28
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:K.28
1PE.35: 6 residues within 4Å:- Chain D: N.366, K.368, R.451, D.460, E.481, Q.484
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:K.368
1PE.45: 3 residues within 4Å:- Chain E: Y.20, E.233, K.237
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:K.237
- Hydrogen bonds: E:K.237
1PE.46: 6 residues within 4Å:- Chain E: Y.20, H.25, F.206, K.237, L.238, Y.328
1 PLIP interactions:1 interactions with chain E- Water bridges: E:T.332
1PE.47: 4 residues within 4Å:- Chain E: N.366, K.368, D.460
- Chain F: S.171
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:K.368
1PE.54: 7 residues within 4Å:- Chain F: Y.20, N.21, H.25, F.206, K.237, Y.328
- Ligands: 1PE.55
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:N.21
1PE.55: 5 residues within 4Å:- Chain F: Y.20, E.233, K.237
- Ligands: SO4.53, 1PE.54
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:E.233, F:K.237
1PE.56: 5 residues within 4Å:- Chain D: S.171
- Chain F: N.366, K.368, D.460, Q.484
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain F- Hydrogen bonds: D:S.171, F:K.368
1PE.57: 6 residues within 4Å:- Chain A: E.424, W.443
- Chain F: L.431, S.434, V.441, W.442
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.424
- 8 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)
2PE.16: 5 residues within 4Å:- Chain B: Y.20, N.21, H.25, K.237, Y.328
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Y.328
2PE.17: 6 residues within 4Å:- Chain B: S.10, L.11, D.12, P.13, T.14, Y.221
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.221, B:Y.221
- Water bridges: B:Q.7
2PE.26: 7 residues within 4Å:- Chain C: Q.7, S.10, L.11, D.12, P.13, T.14, Y.221
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:Y.221, C:Y.221
- Water bridges: C:T.14, C:T.14, C:S.15
2PE.36: 6 residues within 4Å:- Chain D: Y.20, N.21, E.233, Q.236, K.237
- Ligands: SO4.32
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:K.237
- Hydrogen bonds: D:K.237
2PE.37: 6 residues within 4Å:- Chain D: A.2, S.3, E.4, V.5, T.14, N.229
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:V.5, D:N.229
2PE.38: 6 residues within 4Å:- Chain D: S.10, L.11, D.12, P.13, T.14, Y.221
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:Y.221
- Water bridges: D:T.14, D:T.14
2PE.48: 7 residues within 4Å:- Chain E: Q.7, S.10, L.11, D.12, P.13, T.14, Y.221
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Q.7
- Water bridges: E:T.14
2PE.58: 6 residues within 4Å:- Chain F: S.10, L.11, D.12, P.13, T.14, Y.221
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:T.14
- Water bridges: F:T.14
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kannan Sivaraman, K. et al., Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum. J.Med.Chem. (2013)
- Release Date
- 2013-06-12
- Peptides
- M17 leucyl aminopeptidase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 6 x 1OT: {(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid(Non-covalent)
- 11 x SO4: SULFATE ION(Non-functional Binders)
- 15 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 8 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kannan Sivaraman, K. et al., Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum. J.Med.Chem. (2013)
- Release Date
- 2013-06-12
- Peptides
- M17 leucyl aminopeptidase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F