SMTL ID : 8pzm.1

Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14 bound to bestatin inhibitor and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

6 x BES: 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID(Non-covalent)

BES.1: 19 residues within 4Å: Chain A: K.288, D.293, K.300, M.308, D.311, N.368, D.370, E.372, R.374, T.397, L.398, T.399, G.400, I.458, A.487, W.491 Ligands: BCT.3, MN.5, MN.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.458, A:A.487, A:W.491 Hydrogen bonds: A:K.300, A:T.397, A:L.398, A:G.400 Water bridges: A:A.401 BES.7: 19 residues within 4Å: Chain B: K.288, D.293, K.300, M.308, D.311, N.368, D.370, E.372, R.374, T.397, L.398, T.399, G.400, I.458, A.487, W.491 Ligands: BCT.9, MN.11, MN.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.458, B:A.487, B:W.491 Hydrogen bonds: B:K.300, B:T.397, B:L.398, B:G.400 Water bridges: B:A.401 BES.13: 19 residues within 4Å: Chain C: K.288, D.293, K.300, M.308, D.311, N.368, D.370, E.372, R.374, T.397, L.398, T.399, G.400, I.458, A.487, W.491 Ligands: BCT.15, MN.17, MN.18 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.458, C:A.487, C:W.491 Hydrogen bonds: C:K.288, C:K.288, C:D.293, C:K.300, C:L.398, C:G.400 Water bridges: C:A.401 BES.19: 19 residues within 4Å: Chain D: K.288, D.293, K.300, M.308, D.311, N.368, D.370, E.372, R.374, T.397, L.398, T.399, G.400, I.458, A.487, W.491 Ligands: BCT.21, MN.23, MN.24 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.458, D:A.487, D:W.491 Hydrogen bonds: D:K.300, D:T.397, D:L.398, D:G.400 Water bridges: D:A.401 BES.25: 19 residues within 4Å: Chain E: K.288, D.293, K.300, M.308, D.311, N.368, D.370, E.372, R.374, T.397, L.398, T.399, G.400, I.458, A.487, W.491 Ligands: BCT.27, MN.29, MN.30 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.458, E:A.487, E:W.491 Hydrogen bonds: E:K.300, E:T.397, E:L.398, E:G.400 Water bridges: E:A.401 BES.31: 19 residues within 4Å: Chain F: K.288, D.293, K.300, M.308, D.311, N.368, D.370, E.372, R.374, T.397, L.398, T.399, G.400, I.458, A.487, W.491 Ligands: BCT.33, MN.35, MN.36 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.458, F:A.487, F:W.491 Hydrogen bonds: F:K.300, F:T.397, F:L.398, F:G.400 Water bridges: F:A.401

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: F.162, N.212, K.498, G.499 Chain C: P.451, F.452 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:R.208, A:N.212 Hydrogen bonds: C:P.451 EDO.4: 5 residues within 4Å: Chain A: I.355, V.356, T.357 Chain B: Y.165, N.216 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.357, A:T.357, A:T.357, B:N.216 EDO.8: 6 residues within 4Å: Chain A: P.451, F.452 Chain B: F.162, N.212, K.498, G.499 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.451 Water bridges: B:R.208, B:N.212 EDO.10: 5 residues within 4Å: Chain B: I.355, V.356, T.357 Chain C: Y.165, N.216 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.357, B:T.357, B:T.357, C:N.216 EDO.14: 6 residues within 4Å: Chain B: P.451, F.452 Chain C: F.162, N.212, K.498, G.499 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:P.451 Water bridges: C:R.208, C:N.212 EDO.16: 5 residues within 4Å: Chain A: Y.165, N.216 Chain C: I.355, V.356, T.357 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.216, C:T.357, C:T.357, C:T.357 EDO.20: 6 residues within 4Å: Chain D: F.162, N.212, K.498, G.499 Chain F: P.451, F.452 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Water bridges: D:R.208, D:N.212 Hydrogen bonds: F:P.451 EDO.22: 5 residues within 4Å: Chain D: I.355, V.356, T.357 Chain E: Y.165, N.216 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:T.357, D:T.357, E:N.216 EDO.26: 6 residues within 4Å: Chain D: P.451, F.452 Chain E: F.162, N.212, K.498, G.499 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Water bridges: E:R.208, E:N.212 Hydrogen bonds: D:P.451 EDO.28: 5 residues within 4Å: Chain E: I.355, V.356, T.357 Chain F: Y.165, N.216 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:N.216, E:T.357, E:T.357 EDO.32: 6 residues within 4Å: Chain E: P.451, F.452 Chain F: F.162, N.212, K.498, G.499 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:P.451 Water bridges: F:R.208, F:N.212 EDO.34: 5 residues within 4Å: Chain D: Y.165, N.216 Chain F: I.355, V.356, T.357 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:N.216, F:T.357, F:T.357

6 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.3: 10 residues within 4Å: Chain A: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: BES.1, MN.5, MN.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.374, A:R.374, A:L.398 BCT.9: 10 residues within 4Å: Chain B: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: BES.7, MN.11, MN.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.374, B:R.374, B:L.398 BCT.15: 10 residues within 4Å: Chain C: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: BES.13, MN.17, MN.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.374, C:R.374, C:L.398 BCT.21: 10 residues within 4Å: Chain D: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: BES.19, MN.23, MN.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.374, D:R.374, D:L.398 BCT.27: 10 residues within 4Å: Chain E: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: BES.25, MN.29, MN.30 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.374, E:R.374, E:L.398 BCT.33: 10 residues within 4Å: Chain F: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: BES.31, MN.35, MN.36 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.374, F:R.374, F:L.398

12 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 7 residues within 4Å: Chain A: K.288, D.293, D.311, E.372 Ligands: BES.1, BCT.3, MN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.293, A:D.311, A:E.372 MN.6: 7 residues within 4Å: Chain A: D.293, K.300, D.370, E.372 Ligands: BES.1, BCT.3, MN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.293, A:D.370, A:D.370, A:E.372 MN.11: 7 residues within 4Å: Chain B: K.288, D.293, D.311, E.372 Ligands: BES.7, BCT.9, MN.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.293, B:D.311, B:E.372 MN.12: 7 residues within 4Å: Chain B: D.293, K.300, D.370, E.372 Ligands: BES.7, BCT.9, MN.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.293, B:D.370, B:D.370, B:E.372 MN.17: 7 residues within 4Å: Chain C: K.288, D.293, D.311, E.372 Ligands: BES.13, BCT.15, MN.18 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.293, C:D.311, C:E.372 MN.18: 7 residues within 4Å: Chain C: D.293, K.300, D.370, E.372 Ligands: BES.13, BCT.15, MN.17 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.293, C:D.370, C:D.370, C:E.372 MN.23: 7 residues within 4Å: Chain D: K.288, D.293, D.311, E.372 Ligands: BES.19, BCT.21, MN.24 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.293, D:D.311, D:E.372 MN.24: 7 residues within 4Å: Chain D: D.293, K.300, D.370, E.372 Ligands: BES.19, BCT.21, MN.23 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.293, D:D.370, D:D.370, D:E.372 MN.29: 7 residues within 4Å: Chain E: K.288, D.293, D.311, E.372 Ligands: BES.25, BCT.27, MN.30 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.293, E:D.311, E:E.372 MN.30: 7 residues within 4Å: Chain E: D.293, K.300, D.370, E.372 Ligands: BES.25, BCT.27, MN.29 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.293, E:D.370, E:D.370, E:E.372 MN.35: 7 residues within 4Å: Chain F: K.288, D.293, D.311, E.372 Ligands: BES.31, BCT.33, MN.36 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.293, F:D.311, F:E.372 MN.36: 7 residues within 4Å: Chain F: D.293, K.300, D.370, E.372 Ligands: BES.31, BCT.33, MN.35 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.293, F:D.370, F:D.370, F:E.372

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simpson, M.C. et al., Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase. Biochemistry (2023)

Release Date

2023-11-15

Peptides

Probable cytosol aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Probable cytosol aminopeptidase

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