SMTL ID : 3kqx.2 (1 other biounit)

Structure of a protease 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: K.291, D.296, D.316, E.378 Ligands: CO3.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.296, A:D.316, A:E.378, H2O.12, H2O.12 ZN.10: 5 residues within 4Å: Chain B: K.291, D.296, D.316, E.378 Ligands: CO3.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.296, B:D.316, B:E.378, H2O.20 ZN.15: 5 residues within 4Å: Chain C: K.291, D.296, D.316, E.378 Ligands: CO3.16 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.296, C:D.316, C:E.378, H2O.30, H2O.31 ZN.22: 6 residues within 4Å: Chain D: K.291, D.296, D.316, E.378 Ligands: CO3.23, 1PE.27 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.296, D:D.316, D:E.378 ZN.31: 5 residues within 4Å: Chain E: K.291, D.296, D.316, E.378 Ligands: CO3.32 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.296, E:D.316, E:E.378, H2O.55 ZN.42: 5 residues within 4Å: Chain F: K.291, D.296, D.316, E.378 Ligands: CO3.43 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.296, F:D.316, F:E.378, H2O.66

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, T.405 Ligands: ZN.1 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 CO3.11: 8 residues within 4Å: Chain B: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.10 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 CO3.16: 8 residues within 4Å: Chain C: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.15 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.377, C:G.379, C:R.380, C:L.404 Water bridges: C:K.291 CO3.23: 8 residues within 4Å: Chain D: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.377, D:G.379, D:R.380, D:L.404 CO3.32: 8 residues within 4Å: Chain E: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.31 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 CO3.43: 8 residues within 4Å: Chain F: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.42 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.291, F:A.377, F:G.379, F:R.380, F:L.404

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: R.503 Chain C: N.455, N.462, S.466 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.462, C:S.466 Water bridges: C:E.371, C:T.453, C:N.455, C:K.457, C:S.466, C:S.466 Salt bridges: A:R.503 SO4.17: 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 C, 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:K.353, A:K.353, B:K.353 Salt bridges: C:K.353, A:K.353, B:K.353 SO4.24: 4 residues within 4Å: Chain D: N.462, S.466 Chain E: R.503 Ligands: 1PE.41 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D Water bridges: E:R.503, D:S.466 Salt bridges: E:R.503 Hydrogen bonds: D:N.462, D:S.466, D:S.466 SO4.33: 6 residues within 4Å: Chain D: S.352, K.353 Chain E: S.352, K.353 Chain F: S.352, K.353 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 2 interactions with chain D Hydrogen bonds: E:K.353, F:K.353, D:K.353 Salt bridges: E:K.353, D:K.353 SO4.34: 5 residues within 4Å: Chain E: I.18, E.19, Y.20, N.21 Ligands: 1PE.36 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:I.18, E:Y.20, E:N.21

30 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 6 residues within 4Å: Chain A: Y.20, N.21, H.25, F.206, Y.328 Ligands: 1PE.9 Ligand excluded by PLIP 1PE.5: 6 residues within 4Å: Chain A: M.309, F.315, T.403, G.406, L.409, A.494 Ligand excluded by PLIP 1PE.6: 5 residues within 4Å: Chain A: W.442, W.443 Chain F: W.442, W.443 Ligands: 1PE.46 Ligand excluded by PLIP 1PE.7: 5 residues within 4Å: Chain A: Y.32, N.39, E.41, Y.187 Ligands: 1PE.8 Ligand excluded by PLIP 1PE.8: 3 residues within 4Å: Chain A: G.37, N.39 Ligands: 1PE.7 Ligand excluded by PLIP 1PE.9: 6 residues within 4Å: Chain A: Y.20, N.21, E.233, Q.236, K.237 Ligands: 1PE.4 Ligand excluded by PLIP 1PE.13: 7 residues within 4Å: Chain B: M.309, M.313, F.315, T.403, G.406, L.409, A.494 Ligand excluded by PLIP 1PE.14: 5 residues within 4Å: Chain A: E.371, G.373 Chain B: D.311, L.312, W.498 Ligand excluded by PLIP 1PE.18: 5 residues within 4Å: Chain C: Y.20, N.21, E.233, K.237 Ligands: 1PE.19 Ligand excluded by PLIP 1PE.19: 7 residues within 4Å: Chain C: Y.20, N.21, H.25, F.206, K.237, Y.328 Ligands: 1PE.18 Ligand excluded by PLIP 1PE.20: 6 residues within 4Å: Chain C: G.307, M.309, F.315, T.403, G.406, A.494 Ligand excluded by PLIP 1PE.21: 5 residues within 4Å: Chain C: I.446, I.447, N.448, E.449 Chain D: Y.416 Ligand excluded by PLIP 1PE.25: 7 residues within 4Å: Chain D: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328 Ligand excluded by PLIP 1PE.26: 4 residues within 4Å: Chain D: Y.20, E.233, Q.236, K.237 Ligand excluded by PLIP 1PE.27: 12 residues within 4Å: Chain D: D.296, K.303, G.307, M.309, M.313, F.315, D.316, T.403, G.406, L.409, A.494 Ligands: ZN.22 Ligand excluded by PLIP 1PE.28: 7 residues within 4Å: Chain D: N.366, K.368, R.451, D.460, E.481, Q.484 Chain E: S.171 Ligand excluded by PLIP 1PE.29: 6 residues within 4Å: Chain D: H.25, D.26, I.27, K.28, E.199, R.202 Ligand excluded by PLIP 1PE.30: 6 residues within 4Å: Chain D: Y.416, L.431, S.434, K.435, V.441, W.442 Ligand excluded by PLIP 1PE.35: 9 residues within 4Å: Chain E: G.307, M.309, M.313, F.315, T.403, L.404, G.406, Y.410, A.494 Ligand excluded by PLIP 1PE.36: 5 residues within 4Å: Chain E: Y.20, E.233, K.237 Ligands: SO4.34, 1PE.37 Ligand excluded by PLIP 1PE.37: 7 residues within 4Å: Chain E: Y.20, H.25, F.206, K.237, L.238, Y.328 Ligands: 1PE.36 Ligand excluded by PLIP 1PE.38: 6 residues within 4Å: Chain E: N.366, K.368, D.460, E.481, Q.484 Chain F: S.171 Ligand excluded by PLIP 1PE.39: 5 residues within 4Å: Chain E: S.10, L.11, D.12, P.13, T.14 Ligand excluded by PLIP 1PE.40: 5 residues within 4Å: Chain E: Y.416, S.434, K.435, V.441, W.442 Ligand excluded by PLIP 1PE.41: 7 residues within 4Å: Chain D: E.371, V.372, G.373 Chain E: D.311, L.312, W.498 Ligands: SO4.24 Ligand excluded by PLIP 1PE.44: 7 residues within 4Å: Chain F: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328 Ligand excluded by PLIP 1PE.45: 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 PLIP 1PE.46: 6 residues within 4Å: Chain F: Y.416, L.431, S.434, V.441, W.442 Ligands: 1PE.6 Ligand excluded by PLIP 1PE.47: 4 residues within 4Å: Chain F: Y.20, N.21, E.233, K.237 Ligand excluded by PLIP 1PE.48: 10 residues within 4Å: Chain F: G.307, M.309, M.313, F.315, T.403, T.405, G.406, L.409, Y.410, A.494 Ligand excluded by PLIP

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.12: 5 residues within 4Å: Chain B: Y.20, F.206, K.237, L.238, Y.328 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGowan, S. et al., Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-02-02

Peptides

M17 leucyl aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

M17 leucyl aminopeptidase

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