SMTL ID : 8pz0.1

Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: Q.390, S.391, N.417, A.419, L.420, Q.423, H.480 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: R.164, L.206, D.209, L.210, L.213, F.222, Q.226 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: G.45, E.46, G.47, R.48, L.74, A.75, G.76 Ligand excluded by PLIP EDO.4: 10 residues within 4Å: Chain A: A.43, V.44, G.45, R.48, K.49, L.50, G.51, A.100, D.136, L.137 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: Q.390, S.391, N.417, A.419, L.420, Q.423, H.480 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: R.164, L.206, D.209, L.210, L.213, F.222, Q.226 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: G.45, E.46, G.47, R.48, L.74, A.75, G.76 Ligand excluded by PLIP EDO.19: 10 residues within 4Å: Chain B: A.43, V.44, G.45, R.48, K.49, L.50, G.51, A.100, D.136, L.137 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain C: Q.390, S.391, N.417, A.419, L.420, Q.423, H.480 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain C: R.164, L.206, D.209, L.210, L.213, F.222, Q.226 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain C: G.45, E.46, G.47, R.48, L.74, A.75, G.76 Ligand excluded by PLIP EDO.34: 10 residues within 4Å: Chain C: A.43, V.44, G.45, R.48, K.49, L.50, G.51, A.100, D.136, L.137 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain D: Q.390, S.391, N.417, A.419, L.420, Q.423, H.480 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain D: R.164, L.206, D.209, L.210, L.213, F.222, Q.226 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain D: G.45, E.46, G.47, R.48, L.74, A.75, G.76 Ligand excluded by PLIP EDO.49: 10 residues within 4Å: Chain D: A.43, V.44, G.45, R.48, K.49, L.50, G.51, A.100, D.136, L.137 Ligand excluded by PLIP EDO.61: 7 residues within 4Å: Chain E: Q.390, S.391, N.417, A.419, L.420, Q.423, H.480 Ligand excluded by PLIP EDO.62: 7 residues within 4Å: Chain E: R.164, L.206, D.209, L.210, L.213, F.222, Q.226 Ligand excluded by PLIP EDO.63: 7 residues within 4Å: Chain E: G.45, E.46, G.47, R.48, L.74, A.75, G.76 Ligand excluded by PLIP EDO.64: 10 residues within 4Å: Chain E: A.43, V.44, G.45, R.48, K.49, L.50, G.51, A.100, D.136, L.137 Ligand excluded by PLIP EDO.76: 7 residues within 4Å: Chain F: Q.390, S.391, N.417, A.419, L.420, Q.423, H.480 Ligand excluded by PLIP EDO.77: 7 residues within 4Å: Chain F: R.164, L.206, D.209, L.210, L.213, F.222, Q.226 Ligand excluded by PLIP EDO.78: 7 residues within 4Å: Chain F: G.45, E.46, G.47, R.48, L.74, A.75, G.76 Ligand excluded by PLIP EDO.79: 10 residues within 4Å: Chain F: A.43, V.44, G.45, R.48, K.49, L.50, G.51, A.100, D.136, L.137 Ligand excluded by PLIP

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

BCT.5: 9 residues within 4Å: Chain A: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: NA.6, NA.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.374, A:R.374, A:L.398 BCT.20: 9 residues within 4Å: Chain B: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: NA.21, NA.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.374, B:R.374, B:L.398 BCT.35: 9 residues within 4Å: Chain C: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: NA.36, NA.40 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.374, C:R.374, C:L.398 BCT.50: 9 residues within 4Å: Chain D: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: NA.51, NA.55 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.374, D:R.374, D:L.398 BCT.65: 9 residues within 4Å: Chain E: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: NA.66, NA.70 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.374, E:R.374, E:L.398 BCT.80: 9 residues within 4Å: Chain F: K.288, D.370, A.371, E.372, G.373, R.374, L.398 Ligands: NA.81, NA.85 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.374, F:R.374, F:L.398

30 x NA: SODIUM ION(Non-functional Binders)

NA.6: 6 residues within 4Å: Chain A: K.288, D.293, D.311, E.372 Ligands: BCT.5, NA.10 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: A.100, G.101, K.102, E.103, L.106 Ligand excluded by PLIP NA.8: 3 residues within 4Å: Chain A: G.107, R.109, Q.110 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: Q.447, G.460, P.461, K.462 Ligand excluded by PLIP NA.10: 6 residues within 4Å: Chain A: D.293, K.300, D.370, E.372 Ligands: BCT.5, NA.6 Ligand excluded by PLIP NA.21: 6 residues within 4Å: Chain B: K.288, D.293, D.311, E.372 Ligands: BCT.20, NA.25 Ligand excluded by PLIP NA.22: 5 residues within 4Å: Chain B: A.100, G.101, K.102, E.103, L.106 Ligand excluded by PLIP NA.23: 3 residues within 4Å: Chain B: G.107, R.109, Q.110 Ligand excluded by PLIP NA.24: 4 residues within 4Å: Chain B: Q.447, G.460, P.461, K.462 Ligand excluded by PLIP NA.25: 6 residues within 4Å: Chain B: D.293, K.300, D.370, E.372 Ligands: BCT.20, NA.21 Ligand excluded by PLIP NA.36: 6 residues within 4Å: Chain C: K.288, D.293, D.311, E.372 Ligands: BCT.35, NA.40 Ligand excluded by PLIP NA.37: 5 residues within 4Å: Chain C: A.100, G.101, K.102, E.103, L.106 Ligand excluded by PLIP NA.38: 3 residues within 4Å: Chain C: G.107, R.109, Q.110 Ligand excluded by PLIP NA.39: 4 residues within 4Å: Chain C: Q.447, G.460, P.461, K.462 Ligand excluded by PLIP NA.40: 6 residues within 4Å: Chain C: D.293, K.300, D.370, E.372 Ligands: BCT.35, NA.36 Ligand excluded by PLIP NA.51: 6 residues within 4Å: Chain D: K.288, D.293, D.311, E.372 Ligands: BCT.50, NA.55 Ligand excluded by PLIP NA.52: 5 residues within 4Å: Chain D: A.100, G.101, K.102, E.103, L.106 Ligand excluded by PLIP NA.53: 3 residues within 4Å: Chain D: G.107, R.109, Q.110 Ligand excluded by PLIP NA.54: 4 residues within 4Å: Chain D: Q.447, G.460, P.461, K.462 Ligand excluded by PLIP NA.55: 6 residues within 4Å: Chain D: D.293, K.300, D.370, E.372 Ligands: BCT.50, NA.51 Ligand excluded by PLIP NA.66: 6 residues within 4Å: Chain E: K.288, D.293, D.311, E.372 Ligands: BCT.65, NA.70 Ligand excluded by PLIP NA.67: 5 residues within 4Å: Chain E: A.100, G.101, K.102, E.103, L.106 Ligand excluded by PLIP NA.68: 3 residues within 4Å: Chain E: G.107, R.109, Q.110 Ligand excluded by PLIP NA.69: 4 residues within 4Å: Chain E: Q.447, G.460, P.461, K.462 Ligand excluded by PLIP NA.70: 6 residues within 4Å: Chain E: D.293, K.300, D.370, E.372 Ligands: BCT.65, NA.66 Ligand excluded by PLIP NA.81: 6 residues within 4Å: Chain F: K.288, D.293, D.311, E.372 Ligands: BCT.80, NA.85 Ligand excluded by PLIP NA.82: 5 residues within 4Å: Chain F: A.100, G.101, K.102, E.103, L.106 Ligand excluded by PLIP NA.83: 3 residues within 4Å: Chain F: G.107, R.109, Q.110 Ligand excluded by PLIP NA.84: 4 residues within 4Å: Chain F: Q.447, G.460, P.461, K.462 Ligand excluded by PLIP NA.85: 6 residues within 4Å: Chain F: D.293, K.300, D.370, E.372 Ligands: BCT.80, NA.81 Ligand excluded by PLIP

30 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Chain A: K.426, A.427, Q.510, E.514 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: T.221, G.224, E.225, V.241, R.267 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: P.265, R.267 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: G.407, S.408, N.409 Chain F: Y.444, Q.447 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: A.185, D.186 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain B: K.426, A.427, Q.510, E.514 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain B: T.221, G.224, E.225, V.241, R.267 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: P.265, R.267 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain B: G.407, S.408, N.409 Chain E: Y.444, Q.447 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: A.185, D.186 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain C: K.426, A.427, Q.510, E.514 Ligand excluded by PLIP CL.42: 5 residues within 4Å: Chain C: T.221, G.224, E.225, V.241, R.267 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain C: P.265, R.267 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain C: G.407, S.408, N.409 Chain D: Y.444, Q.447 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain C: A.185, D.186 Ligand excluded by PLIP CL.56: 4 residues within 4Å: Chain D: K.426, A.427, Q.510, E.514 Ligand excluded by PLIP CL.57: 5 residues within 4Å: Chain D: T.221, G.224, E.225, V.241, R.267 Ligand excluded by PLIP CL.58: 2 residues within 4Å: Chain D: P.265, R.267 Ligand excluded by PLIP CL.59: 5 residues within 4Å: Chain C: Y.444, Q.447 Chain D: G.407, S.408, N.409 Ligand excluded by PLIP CL.60: 2 residues within 4Å: Chain D: A.185, D.186 Ligand excluded by PLIP CL.71: 4 residues within 4Å: Chain E: K.426, A.427, Q.510, E.514 Ligand excluded by PLIP CL.72: 5 residues within 4Å: Chain E: T.221, G.224, E.225, V.241, R.267 Ligand excluded by PLIP CL.73: 2 residues within 4Å: Chain E: P.265, R.267 Ligand excluded by PLIP CL.74: 5 residues within 4Å: Chain B: Y.444, Q.447 Chain E: G.407, S.408, N.409 Ligand excluded by PLIP CL.75: 2 residues within 4Å: Chain E: A.185, D.186 Ligand excluded by PLIP CL.86: 4 residues within 4Å: Chain F: K.426, A.427, Q.510, E.514 Ligand excluded by PLIP CL.87: 5 residues within 4Å: Chain F: T.221, G.224, E.225, V.241, R.267 Ligand excluded by PLIP CL.88: 2 residues within 4Å: Chain F: P.265, R.267 Ligand excluded by PLIP CL.89: 5 residues within 4Å: Chain A: Y.444, Q.447 Chain F: G.407, S.408, N.409 Ligand excluded by PLIP CL.90: 2 residues within 4Å: Chain F: A.185, D.186 Ligand excluded by PLIP

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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