SMTL ID : 3t8w.1 (1 other biounit)

A bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.1: 9 residues within 4Å: Chain A: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.3, DGZ.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.378, A:R.380, A:R.380, A:R.380 CO3.9: 9 residues within 4Å: Chain B: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.11, DGZ.12 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 CO3.14: 9 residues within 4Å: Chain C: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.15, DGZ.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.377, C:G.379, C:R.380, C:L.404 CO3.25: 9 residues within 4Å: Chain D: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.26, DGZ.28 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.377, D:G.379, D:R.380, D:L.404 CO3.35: 8 residues within 4Å: Chain E: K.291, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.36, DGZ.38 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.378, E:G.379, E:R.380, E:R.380 CO3.45: 9 residues within 4Å: Chain F: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.46, DGZ.48 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.376, F:G.379, F:R.380

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)

2PE.13: 5 residues within 4Å: Chain B: Y.20, N.21, H.25, K.237, Y.328 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.21, B:Y.328

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
A

B
B

C
C

D
D

E
E

F
F

M17 leucyl aminopeptidase

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