SMTL ID : 1bll.1

X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE STRUCTURE OF BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH AMASTATIN: FORMULATION OF A CATALYTIC MECHANISM FEATURING A GEM-DIOLATE TRANSITION STATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x L2O- VAL- VAL- ASP: AMASTATIN(Non-covalent)

L2O-VAL-VAL-ASP.1: 20 residues within 4Å: Chain A: K.251, D.256, K.263, M.271, D.274, D.333, E.335, R.337, T.360, L.361, T.362, G.363, A.364, I.367, R.426, G.429 Chain E: I.367 Ligands: ZN.2, ZN.3, L2O-VAL-VAL-ASP.13 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.251, A:K.251, A:D.256, A:D.256, A:K.263, A:R.337, A:R.337, A:L.361, A:G.363, A:G.429 Water bridges: A:A.364, A:A.364 L2O-VAL-VAL-ASP.4: 20 residues within 4Å: Chain B: K.251, D.256, K.263, M.271, D.274, D.333, E.335, R.337, T.360, L.361, T.362, G.363, A.364, I.367, R.426, G.429 Chain D: I.367 Ligands: ZN.5, ZN.6, L2O-VAL-VAL-ASP.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.251, B:K.251, B:D.256, B:D.256, B:K.263, B:R.337, B:R.337, B:L.361, B:G.363, B:G.429 Water bridges: B:A.364, B:A.364 L2O-VAL-VAL-ASP.7: 20 residues within 4Å: Chain C: K.251, D.256, K.263, M.271, D.274, D.333, E.335, R.337, T.360, L.361, T.362, G.363, A.364, I.367, R.426, G.429 Chain F: I.367 Ligands: ZN.8, ZN.9, L2O-VAL-VAL-ASP.16 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.251, C:K.251, C:D.256, C:D.256, C:K.263, C:R.337, C:R.337, C:L.361, C:G.363, C:G.429 Water bridges: C:A.364, C:A.364 L2O-VAL-VAL-ASP.10: 20 residues within 4Å: Chain B: I.367 Chain D: K.251, D.256, K.263, M.271, D.274, D.333, E.335, R.337, T.360, L.361, T.362, G.363, A.364, I.367, R.426, G.429 Ligands: L2O-VAL-VAL-ASP.4, ZN.11, ZN.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:K.251, D:K.251, D:D.256, D:K.263, D:R.337, D:R.337, D:L.361, D:G.363, D:G.363, D:G.429 Water bridges: D:A.364, D:A.364 L2O-VAL-VAL-ASP.13: 20 residues within 4Å: Chain A: I.367 Chain E: K.251, D.256, K.263, M.271, D.274, D.333, E.335, R.337, T.360, L.361, T.362, G.363, A.364, I.367, R.426, G.429 Ligands: L2O-VAL-VAL-ASP.1, ZN.14, ZN.15 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:K.251, E:K.251, E:D.256, E:K.263, E:R.337, E:R.337, E:L.361, E:G.363, E:G.363, E:G.429 Water bridges: E:A.364, E:A.364 L2O-VAL-VAL-ASP.16: 20 residues within 4Å: Chain C: I.367 Chain F: K.251, D.256, K.263, M.271, D.274, D.333, E.335, R.337, T.360, L.361, T.362, G.363, A.364, I.367, R.426, G.429 Ligands: L2O-VAL-VAL-ASP.7, ZN.17, ZN.18 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:K.251, F:K.251, F:D.256, F:K.263, F:R.337, F:R.337, F:L.361, F:G.363, F:G.363, F:G.429 Water bridges: F:A.364, F:A.364

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.256, D.333, E.335 Ligands: L2O-VAL-VAL-ASP.1, L2O-VAL-VAL-ASP.1, ZN.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.256, A:D.256, A:D.333, A:D.333, A:E.335 ZN.3: 6 residues within 4Å: Chain A: K.251, D.256, D.274, E.335 Ligands: L2O-VAL-VAL-ASP.1, ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.256, A:D.274, A:E.335 ZN.5: 6 residues within 4Å: Chain B: D.256, D.333, E.335 Ligands: L2O-VAL-VAL-ASP.4, L2O-VAL-VAL-ASP.4, ZN.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.256, B:D.256, B:D.333, B:D.333, B:E.335 ZN.6: 6 residues within 4Å: Chain B: K.251, D.256, D.274, E.335 Ligands: L2O-VAL-VAL-ASP.4, ZN.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.256, B:D.274, B:E.335 ZN.8: 6 residues within 4Å: Chain C: D.256, D.333, E.335 Ligands: L2O-VAL-VAL-ASP.7, L2O-VAL-VAL-ASP.7, ZN.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.256, C:D.256, C:D.333, C:D.333, C:E.335 ZN.9: 6 residues within 4Å: Chain C: K.251, D.256, D.274, E.335 Ligands: L2O-VAL-VAL-ASP.7, ZN.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.256, C:D.274, C:E.335 ZN.11: 6 residues within 4Å: Chain D: D.256, D.333, E.335 Ligands: L2O-VAL-VAL-ASP.10, L2O-VAL-VAL-ASP.10, ZN.12 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.256, D:D.256, D:D.333, D:D.333, D:E.335 ZN.12: 6 residues within 4Å: Chain D: K.251, D.256, D.274, E.335 Ligands: L2O-VAL-VAL-ASP.10, ZN.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.256, D:D.274, D:E.335 ZN.14: 6 residues within 4Å: Chain E: D.256, D.333, E.335 Ligands: L2O-VAL-VAL-ASP.13, L2O-VAL-VAL-ASP.13, ZN.15 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.256, E:D.256, E:D.333, E:D.333, E:E.335 ZN.15: 6 residues within 4Å: Chain E: K.251, D.256, D.274, E.335 Ligands: L2O-VAL-VAL-ASP.13, ZN.14 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.256, E:D.274, E:E.335 ZN.17: 6 residues within 4Å: Chain F: D.256, D.333, E.335 Ligands: L2O-VAL-VAL-ASP.16, L2O-VAL-VAL-ASP.16, ZN.18 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.256, F:D.256, F:D.333, F:D.333, F:E.335 ZN.18: 6 residues within 4Å: Chain F: K.251, D.256, D.274, E.335 Ligands: L2O-VAL-VAL-ASP.16, ZN.17 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.256, F:D.274, F:E.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H. et al., X-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state. Biochemistry (1993)

Release Date

1994-01-31

Peptides

LEUCINE AMINOPEPTIDASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
E

C
E

D
E

E
E

F
E

LEUCINE AMINOPEPTIDASE