- 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: 7 residues within 4Å:- Chain A: K.291, D.296, D.316, E.378
- Ligands: CO3.1, ZN.3, 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.3: 6 residues within 4Å:- Chain A: D.296, K.303, D.376, E.378
- Ligands: ZN.2, 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.14: 7 residues within 4Å:- Chain B: K.291, D.296, D.316, E.378
- Ligands: CO3.13, ZN.15, DGZ.16
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.296, B:D.316, B:E.378
ZN.15: 6 residues within 4Å:- Chain B: D.296, K.303, D.376, E.378
- Ligands: ZN.14, DGZ.16
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.296, B:D.376, B:D.376, B:E.378
ZN.22: 7 residues within 4Å:- Chain C: K.291, D.296, D.316, E.378
- Ligands: CO3.21, ZN.23, DGZ.24
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.296, C:D.316, C:D.316, C:E.378
ZN.23: 6 residues within 4Å:- Chain C: D.296, K.303, D.376, E.378
- Ligands: ZN.22, DGZ.24
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.296, C:D.376, C:D.376, C:E.378
ZN.34: 7 residues within 4Å:- Chain D: K.291, D.296, D.316, E.378
- Ligands: CO3.33, ZN.35, DGZ.36
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.296, D:D.316, D:D.316, D:E.378
ZN.35: 6 residues within 4Å:- Chain D: D.296, K.303, D.376, E.378
- Ligands: ZN.34, DGZ.36
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.296, D:D.376, D:D.376, D:E.378
ZN.45: 7 residues within 4Å:- Chain E: K.291, D.296, D.316, E.378
- Ligands: CO3.44, ZN.46, DGZ.47
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:D.296, E:D.316, E:D.316, E:E.378
ZN.46: 6 residues within 4Å:- Chain E: D.296, K.303, D.376, E.378
- Ligands: ZN.45, DGZ.47
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:D.296, E:D.376, E:D.376, E:E.378
ZN.54: 6 residues within 4Å:- Chain F: D.296, K.303, D.376, E.378
- Ligands: ZN.55, DGZ.56
4 PLIP interactions:4 interactions with chain F- Metal complexes: F:D.296, F:D.376, F:D.376, F:E.378
ZN.55: 7 residues within 4Å:- Chain F: K.291, D.296, D.316, E.378
- Ligands: CO3.53, ZN.54, DGZ.56
4 PLIP interactions:4 interactions with chain F- Metal complexes: F:D.296, F:D.316, F:D.316, 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: 31 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, E.378, R.380, T.403, L.404, T.405, G.406, A.407, L.409, Y.410, I.464, S.465, S.471, A.494
- Chain F: Y.410, S.467
- Ligands: CO3.1, ZN.2, ZN.3, DGZ.56
15 PLIP interactions:14 interactions with chain A, 1 interactions with chain F- Hydrophobic interactions: A:A.305, A:F.315, A:N.374, 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:A.407
- pi-Stacking: F:Y.410
DGZ.16: 33 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, S.467, V.468, A.494
- Chain E: Y.410, K.469
- Ligands: CO3.13, ZN.14, ZN.15, DGZ.47
16 PLIP interactions:15 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, B:A.494
- Hydrogen bonds: B:K.303, B:G.307, B:T.403, B:L.404, B:G.406, B:Y.410
- Water bridges: B:S.471
- pi-Stacking: E:Y.410
DGZ.24: 31 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, 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.471, A.494
- Chain D: Y.410
- Ligands: CO3.21, ZN.22, ZN.23, DGZ.36
16 PLIP interactions:15 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:A.305, C:F.315, C:A.377, C:L.409, C:Y.410, C:I.464, C:A.494
- Hydrogen bonds: C:K.303, C:G.307, C:T.403, C:L.404, C:G.406, C:Y.410
- Water bridges: C:A.407, C:A.407
- pi-Stacking: D:Y.410
DGZ.36: 32 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, 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
- Ligands: DGZ.24, CO3.33, ZN.34, ZN.35
16 PLIP interactions:15 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:A.305, D:F.315, D:N.374, D:A.377, D:L.409, D:Y.410, D:I.464, D:A.494, C:Y.410
- Hydrogen bonds: D:K.291, D:K.303, D:G.307, D:T.403, D:L.404, D:G.406
- Water bridges: D:A.407
DGZ.47: 32 residues within 4Å:- Chain B: Y.410, S.467, V.468
- 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, A.494
- Ligands: DGZ.16, CO3.44, ZN.45, ZN.46
14 PLIP interactions:1 interactions with chain B, 13 interactions with chain E- pi-Stacking: B:Y.410
- 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
DGZ.56: 30 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, A.494
- Ligands: DGZ.4, CO3.53, ZN.54, ZN.55
17 PLIP interactions:16 interactions with chain F, 1 interactions with chain A- Hydrophobic interactions: F:A.305, F:F.315, F:N.374, F:A.377, F:L.409, F:Y.410, F:I.464, F:A.494
- Hydrogen bonds: F:K.303, F:G.307, F:T.403, F:L.404, F:G.406
- Water bridges: F:S.471, F:S.471, F:S.471
- pi-Stacking: A:Y.410
- 17 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.12
Ligand excluded by PLIPSO4.6: 8 residues within 4Å:- Chain A: F.73, N.78, F.82, F.92
- Chain D: Y.93, M.94, F.95, S.101
Ligand excluded by PLIPSO4.7: 5 residues within 4Å:- Chain A: E.42, G.43, L.136, S.137, K.138
Ligand excluded by PLIPSO4.8: 8 residues within 4Å:- Chain A: Y.161, D.166, Y.209, S.212, A.216, K.504, P.505
- Chain C: Y.458
Ligand excluded by PLIPSO4.17: 6 residues within 4Å:- Chain A: S.352, K.353
- Chain B: S.352, K.353
- Chain C: S.352, K.353
Ligand excluded by PLIPSO4.18: 5 residues within 4Å:- Chain B: S.3, E.4, V.5, T.14, N.229
Ligand excluded by PLIPSO4.19: 8 residues within 4Å:- Chain A: Y.458
- Chain B: Y.161, D.166, Y.209, S.212, A.216, K.504, P.505
Ligand excluded by PLIPSO4.25: 5 residues within 4Å:- Chain C: I.18, E.19, Y.20, N.21
- Ligands: 1PE.30
Ligand excluded by PLIPSO4.26: 9 residues within 4Å:- Chain C: F.73, N.78, K.81, F.82, F.92
- Chain E: Y.93, M.94, F.95, S.101
Ligand excluded by PLIPSO4.27: 8 residues within 4Å:- Chain C: L.131, H.132, D.133, N.134, Y.163, N.177, M.178, E.179
Ligand excluded by PLIPSO4.28: 5 residues within 4Å:- Chain C: E.42, G.43, L.136, S.137, K.138
Ligand excluded by PLIPSO4.29: 5 residues within 4Å:- Chain C: S.3, E.4, V.5, T.14, N.229
Ligand excluded by PLIPSO4.37: 6 residues within 4Å:- Chain D: S.352, K.353
- Chain E: S.352, K.353
- Chain F: S.352, K.353
Ligand excluded by PLIPSO4.38: 5 residues within 4Å:- Chain D: I.18, E.19, Y.20, N.21
- Ligands: 1PE.41
Ligand excluded by PLIPSO4.39: 5 residues within 4Å:- Chain D: S.3, E.4, V.5, T.14, N.229
Ligand excluded by PLIPSO4.48: 5 residues within 4Å:- Chain E: I.18, E.19, Y.20, N.21
- Ligands: 1PE.49
Ligand excluded by PLIPSO4.57: 5 residues within 4Å:- Chain F: S.3, E.4, V.5, T.14, N.229
Ligand excluded by PLIP- 19 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.9: 7 residues within 4Å:- Chain A: Y.20, N.21, H.25, F.206, K.237, Y.328
- Ligands: 1PE.12
Ligand excluded by PLIP1PE.10: 5 residues within 4Å:- Chain A: Y.32, N.39, E.41, Y.187
- Ligands: 1PE.11
Ligand excluded by PLIP1PE.11: 5 residues within 4Å:- Chain A: Y.32, G.37, N.39, Y.187
- Ligands: 1PE.10
Ligand excluded by PLIP1PE.12: 7 residues within 4Å:- Chain A: Y.20, N.21, E.233, Q.236, K.237
- Ligands: SO4.5, 1PE.9
Ligand excluded by PLIP1PE.30: 5 residues within 4Å:- Chain C: Y.20, E.233, Q.236, K.237
- Ligands: SO4.25
Ligand excluded by PLIP1PE.31: 6 residues within 4Å:- Chain C: Y.20, N.21, H.25, F.206, K.237, Y.328
Ligand excluded by PLIP1PE.32: 5 residues within 4Å:- Chain C: I.446, I.447, N.448, E.449
- Chain D: Y.416
Ligand excluded by PLIP1PE.40: 7 residues within 4Å:- Chain D: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328
Ligand excluded by PLIP1PE.41: 5 residues within 4Å:- Chain D: Y.20, E.233, Q.236, K.237
- Ligands: SO4.38
Ligand excluded by PLIP1PE.42: 7 residues within 4Å:- Chain D: N.366, G.367, K.368, R.451, D.460, E.481
- Chain E: S.171
Ligand excluded by PLIP1PE.43: 5 residues within 4Å:- Chain D: L.431, S.434, K.435, V.441, W.442
Ligand excluded by PLIP1PE.49: 4 residues within 4Å:- Chain E: Y.20, E.233, K.237
- Ligands: SO4.48
Ligand excluded by PLIP1PE.50: 6 residues within 4Å:- Chain E: Y.20, N.21, H.25, F.206, K.237, Y.328
Ligand excluded by PLIP1PE.51: 7 residues within 4Å:- Chain E: N.366, K.368, R.451, D.460, E.481, Q.484
- Chain F: S.171
Ligand excluded by PLIP1PE.52: 5 residues within 4Å:- Chain E: S.10, L.11, D.12, P.13, T.14
Ligand excluded by PLIP1PE.58: 7 residues within 4Å:- Chain F: Y.20, N.21, H.25, F.206, K.237, Y.328
- Ligands: 1PE.61
Ligand excluded by PLIP1PE.59: 7 residues within 4Å:- Chain D: S.171
- Chain F: N.366, K.368, R.451, D.460, E.481, Q.484
Ligand excluded by PLIP1PE.60: 5 residues within 4Å:- Chain A: W.442, W.443
- Chain F: L.431, W.442, W.443
Ligand excluded by PLIP1PE.61: 5 residues within 4Å:- Chain F: Y.20, N.21, E.233, K.237
- Ligands: 1PE.58
Ligand excluded by PLIP- 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
GB
HC
ID
JE
KF
L
- 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)
- 17 x SO4: SULFATE ION(Non-functional Binders)
- 19 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
GB
HC
ID
JE
KF
L