- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 12 x ZN: ZINC ION(Non-covalent)
ZN.2: 6 residues within 4Å:- Chain A: D.296, K.303, D.376, E.378
- Ligands: ZN.3, DGZ.4
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.296, A:D.376, A:D.376, A:E.378
ZN.3: 7 residues within 4Å:- Chain A: K.291, D.296, D.316, E.378
- Ligands: CO3.1, ZN.2, DGZ.4
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.296, A:D.316, A:D.316, A:E.378
ZN.10: 6 residues within 4Å:- Chain B: D.296, K.303, D.376, E.378
- Ligands: ZN.11, DGZ.12
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.296, B:D.376, B:D.376, B:E.378
ZN.11: 7 residues within 4Å:- Chain B: K.291, D.296, D.316, E.378
- Ligands: CO3.9, ZN.10, DGZ.12
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.296, B:D.316, B:E.378
ZN.15: 7 residues within 4Å:- Chain C: K.291, D.296, D.316, E.378
- Ligands: CO3.14, ZN.16, DGZ.17
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.296, C:D.316, C:D.316, C:E.378
ZN.16: 6 residues within 4Å:- Chain C: D.296, K.303, D.376, E.378
- Ligands: ZN.15, DGZ.17
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.296, C:D.376, C:D.376, C:E.378
ZN.26: 7 residues within 4Å:- Chain D: K.291, D.296, D.316, E.378
- Ligands: CO3.25, ZN.27, DGZ.28
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.296, D:D.316, D:E.378
ZN.27: 6 residues within 4Å:- Chain D: D.296, K.303, D.376, E.378
- Ligands: ZN.26, DGZ.28
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.296, D:D.376, D:D.376, D:E.378
ZN.36: 7 residues within 4Å:- Chain E: K.291, D.296, D.316, E.378
- Ligands: CO3.35, ZN.37, DGZ.38
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:D.296, E:D.316, E:D.316, E:E.378
ZN.37: 6 residues within 4Å:- Chain E: D.296, K.303, D.376, E.378
- Ligands: ZN.36, DGZ.38
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:D.296, E:D.376, E:D.376, E:E.378
ZN.46: 7 residues within 4Å:- Chain F: K.291, D.296, D.316, E.378
- Ligands: CO3.45, ZN.47, DGZ.48
3 PLIP interactions:3 interactions with chain F- Metal complexes: F:D.296, F:D.316, F:E.378
ZN.47: 6 residues within 4Å:- Chain F: D.296, K.303, D.376, E.378
- Ligands: ZN.46, DGZ.48
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
- 6 x DGZ: N-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide(Non-covalent)
DGZ.4: 33 residues within 4Å:- Chain A: K.291, D.296, K.303, A.305, P.306, G.307, M.309, M.313, F.315, D.316, N.374, D.376, A.377, E.378, R.380, T.403, L.404, T.405, G.406, A.407, L.409, Y.410, I.464, S.465, S.467, S.471, A.494
- Chain F: Y.410, K.469
- Ligands: CO3.1, ZN.2, ZN.3, DGZ.48
17 PLIP interactions:16 interactions with chain A, 1 interactions with chain F- Hydrophobic interactions: A:A.305, A:F.315, A:N.374, A:A.377, A:L.409, A:Y.410, A:I.464, A:A.494
- Hydrogen bonds: A:K.303, A:G.307, A:T.403, A:L.404, A:G.406, A:Y.410
- Water bridges: A:S.471, A:S.471
- pi-Stacking: F:Y.410
DGZ.12: 30 residues within 4Å:- Chain B: K.291, D.296, K.303, A.305, P.306, G.307, M.309, M.313, F.315, D.316, N.374, D.376, A.377, E.378, R.380, T.403, L.404, T.405, G.406, A.407, L.409, Y.410, I.464, S.465
- Chain E: Y.410, K.469
- Ligands: CO3.9, ZN.10, ZN.11, DGZ.38
18 PLIP interactions:17 interactions with chain B, 1 interactions with chain E- Hydrophobic interactions: B:A.305, B:F.315, B:N.374, B:A.377, B:L.409, B:Y.410, B:I.464
- Hydrogen bonds: B:K.291, B:K.303, B:G.307, B:T.403, B:L.404, B:G.406, B:Y.410
- Water bridges: B:A.407, B:S.471, B:S.471
- pi-Stacking: E:Y.410
DGZ.17: 29 residues within 4Å:- Chain C: K.291, D.296, K.303, A.305, P.306, G.307, M.309, M.313, F.315, D.316, N.374, D.376, E.378, R.380, T.403, L.404, T.405, G.406, A.407, Y.410, I.464, S.465, S.471, A.494
- Chain D: Y.410
- Ligands: CO3.14, ZN.15, ZN.16, DGZ.28
17 PLIP interactions:16 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:A.305, C:F.315, C:N.374, C:Y.410, C:I.464, C:A.494
- Hydrogen bonds: C:K.291, C:K.303, C:G.307, C:T.403, C:L.404, C:G.406, C:Y.410
- Water bridges: C:K.303, C:A.407, C:S.471
- pi-Stacking: D:Y.410
DGZ.28: 30 residues within 4Å:- Chain C: Y.410
- Chain D: K.291, D.296, K.303, A.305, P.306, G.307, M.309, M.313, F.315, D.316, N.374, D.376, E.378, R.380, T.403, L.404, T.405, G.406, A.407, L.409, Y.410, I.464, S.465, S.467, A.494
- Ligands: DGZ.17, CO3.25, ZN.26, ZN.27
15 PLIP interactions:14 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:A.305, D:F.315, D:N.374, D:L.409, D:Y.410, D:I.464, D:A.494, C:Y.410
- Hydrogen bonds: D:K.303, D:G.307, D:T.403, D:L.404, D:G.406
- Water bridges: D:A.407, D:S.471
DGZ.38: 31 residues within 4Å:- Chain B: Y.410
- Chain E: K.291, D.296, K.303, A.305, P.306, G.307, M.309, M.313, F.315, D.316, N.374, D.376, A.377, E.378, R.380, T.403, L.404, T.405, G.406, A.407, Y.410, I.464, S.465, S.467, S.471, A.494
- Ligands: DGZ.12, CO3.35, ZN.36, ZN.37
15 PLIP interactions:14 interactions with chain E, 1 interactions with chain B- Hydrophobic interactions: E:A.305, E:F.315, E:N.374, E:A.377, E:Y.410, E:I.464, E:A.494
- Hydrogen bonds: E:K.303, E:G.307, E:T.403, E:L.404, E:G.406
- Water bridges: E:A.407, E:S.471
- pi-Stacking: B:Y.410
DGZ.48: 32 residues within 4Å:- Chain A: Y.410
- Chain F: K.291, D.296, K.303, A.305, P.306, G.307, M.309, M.313, F.315, D.316, N.374, D.376, A.377, E.378, R.380, T.403, L.404, T.405, G.406, A.407, L.409, Y.410, I.464, S.465, S.467, V.468, A.494
- Ligands: DGZ.4, CO3.45, ZN.46, ZN.47
15 PLIP interactions:14 interactions with chain F, 1 interactions with chain A- Hydrophobic interactions: F:A.305, F:F.315, F:N.374, F:L.409, F:Y.410, F:I.464, F:V.468, F:A.494
- Hydrogen bonds: F:K.303, F:G.307, F:T.403, F:L.404, F:G.406
- Water bridges: F:A.407
- pi-Stacking: A:Y.410
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 5 residues within 4Å:- Chain A: I.18, E.19, Y.20, N.21
- Ligands: 1PE.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.20, A:N.21, A:N.21
SO4.6: 5 residues within 4Å:- Chain A: E.42, G.43, L.136, S.137
- Chain D: K.81
6 PLIP interactions:2 interactions with chain D, 4 interactions with chain A- Water bridges: D:K.81, A:G.43, A:A.103
- Salt bridges: D:K.81
- Hydrogen bonds: A:G.43, A:S.137
SO4.18: 6 residues within 4Å:- Chain A: S.352, K.353
- Chain B: S.352, K.353
- Chain C: S.352, K.353
9 PLIP interactions:3 interactions with chain C, 4 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: C:K.353, A:K.353, B:K.353
- Water bridges: C:K.353, A:K.353, A:K.353
- Salt bridges: C:K.353, A:K.353, B:K.353
SO4.19: 5 residues within 4Å:- Chain C: E.42, G.43, L.136, S.137
- Chain E: K.81
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain E- Hydrogen bonds: C:G.43, C:S.137, C:S.137
- Salt bridges: E:K.81
SO4.20: 5 residues within 4Å:- Chain C: N.422, N.423, N.485, T.486, A.487
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.423
SO4.21: 8 residues within 4Å:- Chain C: L.131, H.132, D.133, N.134, Y.163, N.177, M.178, E.179
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:D.133, C:N.134, C:E.179
- Water bridges: C:N.175, C:N.175, C:N.177
- Salt bridges: C:H.132
SO4.22: 4 residues within 4Å:- Chain C: I.446, I.447, N.448
- Chain D: Y.416
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:I.446, C:N.448
- Water bridges: C:N.448, C:N.448, C:N.448, C:N.448, C:E.449
SO4.29: 4 residues within 4Å:- Chain D: I.18, E.19, Y.20, N.21
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:Y.20, D:N.21, D:N.21, D:N.21
SO4.30: 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 D, 2 interactions with chain F, 2 interactions with chain E- Hydrogen bonds: D:K.353, F:K.353, E:K.353
- Salt bridges: D:K.353, F:K.353, E:K.353
SO4.39: 5 residues within 4Å:- Chain E: N.422, N.423, N.485, T.486, A.487
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:N.423
- Water bridges: E:N.422
SO4.40: 4 residues within 4Å:- Chain E: E.19, Y.20, N.21
- Ligands: 1PE.42
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:Y.20, E:N.21, E:N.21
SO4.41: 9 residues within 4Å:- Chain C: F.73, N.78, M.79, K.81, F.82
- Chain E: Y.93, M.94, F.95, S.101
4 PLIP interactions:1 interactions with chain E, 3 interactions with chain C- Hydrogen bonds: E:S.101
- Water bridges: C:K.81, C:K.81
- Salt bridges: C:K.81
- 14 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.7: 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.8: 5 residues within 4Å:- Chain A: Y.20, N.21, E.233, K.237
- Ligands: SO4.5
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.237
1PE.23: 5 residues within 4Å:- Chain C: Y.20, N.21, E.233, K.237
- Ligands: 1PE.24
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:K.237
- Hydrogen bonds: C:K.237
1PE.24: 8 residues within 4Å:- Chain C: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328
- Ligands: 1PE.23
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.21, C:Y.328
1PE.31: 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.32: 6 residues within 4Å:- Chain C: W.443
- Chain D: L.431, S.434, K.435, V.441, W.442
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:K.435
1PE.33: 7 residues within 4Å:- Chain D: N.366, K.368, R.451, D.460, E.481, Q.484
- Chain E: S.171
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:K.368, D:Q.484
- Hydrogen bonds: D:K.368
1PE.34: 8 residues within 4Å:- Chain A: F.73, N.78, K.81, F.82
- Chain D: Y.93, M.94, F.95, S.101
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:M.94, D:S.101
1PE.42: 6 residues within 4Å:- Chain E: Y.20, E.233, Q.236, K.237
- Ligands: SO4.40, 1PE.43
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:K.237
- Hydrogen bonds: E:E.233, E:K.237
1PE.43: 8 residues within 4Å:- Chain E: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328
- Ligands: 1PE.42
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:K.237
1PE.44: 6 residues within 4Å:- Chain E: G.367, K.368, R.451, D.460, E.481
- Chain F: S.171
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:K.368, E:R.451, E:E.481, E:E.481
1PE.49: 5 residues within 4Å:- Chain F: Y.20, N.21, H.25, K.237, Y.328
1 PLIP interactions:1 interactions with chain F- Water bridges: F:K.237
1PE.50: 4 residues within 4Å:- Chain F: Y.20, E.233, Q.236, K.237
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:Q.236, F:K.237
1PE.51: 5 residues within 4Å:- Chain D: S.171
- Chain F: N.366, K.368, D.460, Q.484
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:K.368
- Water bridges: F:E.481
- 1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Harbut, M.B. et al., Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases. Proc.Natl.Acad.Sci.USA (2011)
- Release Date
- 2011-09-28
- 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
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x DGZ: N-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide(Non-covalent)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 14 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Harbut, M.B. et al., Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases. Proc.Natl.Acad.Sci.USA (2011)
- Release Date
- 2011-09-28
- Peptides
- M17 leucyl aminopeptidase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F