SMTL ID : 1lam.1

LEUCINE AMINOPEPTIDASE (UNLIGATED)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

18 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.255, D.332, E.334 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.255, A:D.332, A:D.332, A:E.334, H2O.10 ZN.2: 6 residues within 4Å: Chain A: K.250, D.255, D.273, E.334 Ligands: ZN.1, CO3.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.255, A:D.273, A:E.334, H2O.10 ZN.3: 6 residues within 4Å: Chain A: L.170, M.171, T.173, M.178, R.271, M.274 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.170, A:M.171, A:T.173, A:R.271, H2O.3 ZN.8: 4 residues within 4Å: Chain B: D.255, D.332, E.334 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.255, B:D.332, B:D.332, B:E.334, H2O.29 ZN.9: 6 residues within 4Å: Chain B: K.250, D.255, D.273, E.334 Ligands: ZN.8, CO3.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.255, B:D.273, B:E.334, H2O.29 ZN.10: 6 residues within 4Å: Chain B: L.170, M.171, T.173, M.178, R.271, M.274 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.170, B:M.171, B:T.173, B:R.271, H2O.23 ZN.15: 4 residues within 4Å: Chain C: D.255, D.332, E.334 Ligands: ZN.16 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.255, C:D.332, C:D.332, C:E.334, H2O.49 ZN.16: 6 residues within 4Å: Chain C: K.250, D.255, D.273, E.334 Ligands: ZN.15, CO3.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.255, C:D.273, C:E.334, H2O.49 ZN.17: 6 residues within 4Å: Chain C: L.170, M.171, T.173, M.178, R.271, M.274 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:L.170, C:M.171, C:T.173, C:R.271, H2O.42 ZN.22: 4 residues within 4Å: Chain D: D.255, D.332, E.334 Ligands: ZN.23 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.255, D:D.332, D:D.332, D:E.334, H2O.68 ZN.23: 6 residues within 4Å: Chain D: K.250, D.255, D.273, E.334 Ligands: ZN.22, CO3.25 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.255, D:D.273, D:E.334, H2O.68 ZN.24: 6 residues within 4Å: Chain D: L.170, M.171, T.173, M.178, R.271, M.274 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.170, D:M.171, D:T.173, D:R.271, H2O.62 ZN.29: 4 residues within 4Å: Chain E: D.255, D.332, E.334 Ligands: ZN.30 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.255, E:D.332, E:D.332, E:E.334, H2O.88 ZN.30: 6 residues within 4Å: Chain E: K.250, D.255, D.273, E.334 Ligands: ZN.29, CO3.32 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.255, E:D.273, E:E.334, H2O.88 ZN.31: 6 residues within 4Å: Chain E: L.170, M.171, T.173, M.178, R.271, M.274 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:L.170, E:M.171, E:T.173, E:R.271, H2O.82 ZN.36: 4 residues within 4Å: Chain F: D.255, D.332, E.334 Ligands: ZN.37 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.255, F:D.332, F:D.332, F:E.334, H2O.108 ZN.37: 6 residues within 4Å: Chain F: K.250, D.255, D.273, E.334 Ligands: ZN.36, CO3.39 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.255, F:D.273, F:E.334, H2O.108 ZN.38: 6 residues within 4Å: Chain F: L.170, M.171, T.173, M.178, R.271, M.274 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:L.170, F:M.171, F:T.173, F:R.271, H2O.101

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

CO3.4: 8 residues within 4Å: Chain A: K.250, D.332, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.334, A:G.335, A:R.336, A:R.336, A:R.336 CO3.11: 8 residues within 4Å: Chain B: K.250, D.332, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.334, B:G.335, B:R.336, B:R.336, B:R.336 CO3.18: 8 residues within 4Å: Chain C: K.250, D.332, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.334, C:G.335, C:R.336, C:R.336, C:R.336 CO3.25: 8 residues within 4Å: Chain D: K.250, D.332, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.23 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.334, D:G.335, D:R.336, D:R.336, D:R.336 CO3.32: 8 residues within 4Å: Chain E: K.250, D.332, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.30 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.334, E:G.335, E:R.336, E:R.336, E:R.336 CO3.39: 8 residues within 4Å: Chain F: K.250, D.332, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.37 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.334, F:G.335, F:R.336, F:R.336, F:R.336

18 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 6 residues within 4Å: Chain A: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MRD.6: 6 residues within 4Å: Chain A: P.44, L.46, T.51, R.52 Chain D: D.102, L.103 Ligand excluded by PLIP MRD.7: 7 residues within 4Å: Chain A: H.233, Y.234, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MRD.12: 6 residues within 4Å: Chain B: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MRD.13: 6 residues within 4Å: Chain B: P.44, L.46, T.51, R.52 Chain F: D.102, L.103 Ligand excluded by PLIP MRD.14: 7 residues within 4Å: Chain B: H.233, Y.234, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MRD.19: 6 residues within 4Å: Chain C: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MRD.20: 6 residues within 4Å: Chain C: P.44, L.46, T.51, R.52 Chain E: D.102, L.103 Ligand excluded by PLIP MRD.21: 7 residues within 4Å: Chain C: H.233, Y.234, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MRD.26: 6 residues within 4Å: Chain D: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MRD.27: 6 residues within 4Å: Chain A: D.102, L.103 Chain D: P.44, L.46, T.51, R.52 Ligand excluded by PLIP MRD.28: 7 residues within 4Å: Chain D: H.233, Y.234, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MRD.33: 6 residues within 4Å: Chain E: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MRD.34: 6 residues within 4Å: Chain C: D.102, L.103 Chain E: P.44, L.46, T.51, R.52 Ligand excluded by PLIP MRD.35: 7 residues within 4Å: Chain E: H.233, Y.234, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MRD.40: 6 residues within 4Å: Chain F: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MRD.41: 6 residues within 4Å: Chain B: D.102, L.103 Chain F: P.44, L.46, T.51, R.52 Ligand excluded by PLIP MRD.42: 7 residues within 4Å: Chain F: H.233, Y.234, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strater, N. et al., Two-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography. Biochemistry (1995)

Release Date

1995-10-15

Peptides

LEUCINE AMINOPEPTIDASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

LEUCINE AMINOPEPTIDASE

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