SMTL ID : 2ewb.1

The crystal structure of Bovine Lens Leucine Aminopeptidase in complex with zofenoprilat

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.255, K.262, D.332, E.334 Ligands: ZN.2, ZED.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.255, A:D.332, A:D.332, A:E.334 ZN.2: 7 residues within 4Å: Chain A: K.250, D.255, D.273, E.334 Ligands: ZN.1, CO3.4, ZED.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.255, A:D.273, A:D.273, A:E.334 ZN.10: 6 residues within 4Å: Chain B: D.255, K.262, D.332, E.334 Ligands: ZN.11, ZED.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.255, B:D.332, B:D.332, B:E.334 ZN.11: 7 residues within 4Å: Chain B: K.250, D.255, D.273, E.334 Ligands: ZN.10, CO3.13, ZED.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.255, B:D.273, B:D.273, B:E.334 ZN.19: 6 residues within 4Å: Chain C: D.255, K.262, D.332, E.334 Ligands: ZN.20, ZED.23 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.255, C:D.332, C:D.332, C:E.334 ZN.20: 7 residues within 4Å: Chain C: K.250, D.255, D.273, E.334 Ligands: ZN.19, CO3.22, ZED.23 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.255, C:D.273, C:D.273, C:E.334 ZN.28: 6 residues within 4Å: Chain D: D.255, K.262, D.332, E.334 Ligands: ZN.29, ZED.32 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.255, D:D.332, D:D.332, D:E.334 ZN.29: 7 residues within 4Å: Chain D: K.250, D.255, D.273, E.334 Ligands: ZN.28, CO3.31, ZED.32 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.255, D:D.273, D:D.273, D:E.334 ZN.37: 6 residues within 4Å: Chain E: D.255, K.262, D.332, E.334 Ligands: ZN.38, ZED.41 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.255, E:D.332, E:D.332, E:E.334 ZN.38: 7 residues within 4Å: Chain E: K.250, D.255, D.273, E.334 Ligands: ZN.37, CO3.40, ZED.41 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.255, E:D.273, E:D.273, E:E.334 ZN.46: 6 residues within 4Å: Chain F: D.255, K.262, D.332, E.334 Ligands: ZN.47, ZED.50 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.255, F:D.332, F:D.332, F:E.334 ZN.47: 7 residues within 4Å: Chain F: K.250, D.255, D.273, E.334 Ligands: ZN.46, CO3.49, ZED.50 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.255, F:D.273, F:D.273, F:E.334

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

NA.3: 6 residues within 4Å: Chain A: L.170, M.171, T.173, M.178, R.271, M.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.173 NA.12: 6 residues within 4Å: Chain B: L.170, M.171, T.173, M.178, R.271, M.274 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.171 NA.21: 6 residues within 4Å: Chain C: L.170, M.171, T.173, M.178, R.271, M.274 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.170 NA.30: 6 residues within 4Å: Chain D: L.170, M.171, T.173, M.178, R.271, M.274 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.171 NA.39: 6 residues within 4Å: Chain E: L.170, M.171, T.173, M.178, R.271, M.274 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.271 NA.48: 6 residues within 4Å: Chain F: L.170, M.171, T.173, M.178, R.271, M.274 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:M.171

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

CO3.4: 8 residues within 4Å: Chain A: K.250, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.2, ZED.5 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 CO3.13: 8 residues within 4Å: Chain B: K.250, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.11, ZED.14 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 CO3.22: 8 residues within 4Å: Chain C: K.250, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.20, ZED.23 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 CO3.31: 8 residues within 4Å: Chain D: K.250, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.29, ZED.32 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 CO3.40: 8 residues within 4Å: Chain E: K.250, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.38, ZED.41 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 CO3.49: 8 residues within 4Å: Chain F: K.250, A.333, E.334, G.335, R.336, L.360 Ligands: ZN.47, ZED.50 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

6 x ZED: L-PROLINE, 1-[(2S)-3-MERCAPTO-2-METHYL-1-OXOPROPYL]-4-(PHENYLTHIO)-, 4S(Non-covalent)

ZED.5: 17 residues within 4Å: Chain A: K.250, D.255, K.262, M.270, D.273, N.330, D.332, A.333, E.334, R.336, L.360, T.361, G.362, I.421 Ligands: ZN.1, ZN.2, CO3.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.332, A:I.421, A:I.421 Hydrogen bonds: A:K.262, A:D.332 Water bridges: A:G.362 Salt bridges: A:K.262 ZED.14: 17 residues within 4Å: Chain B: K.250, D.255, K.262, M.270, D.273, N.330, D.332, A.333, E.334, R.336, L.360, T.361, G.362, I.421 Ligands: ZN.10, ZN.11, CO3.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.332, B:I.421, B:I.421 Hydrogen bonds: B:K.262, B:D.332 Water bridges: B:G.362 Salt bridges: B:K.262 ZED.23: 17 residues within 4Å: Chain C: K.250, D.255, K.262, M.270, D.273, N.330, D.332, A.333, E.334, R.336, L.360, T.361, G.362, I.421 Ligands: ZN.19, ZN.20, CO3.22 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:D.332, C:I.421, C:I.421 Hydrogen bonds: C:K.262, C:D.332 Water bridges: C:G.362 Salt bridges: C:K.262 ZED.32: 17 residues within 4Å: Chain D: K.250, D.255, K.262, M.270, D.273, N.330, D.332, A.333, E.334, R.336, L.360, T.361, G.362, I.421 Ligands: ZN.28, ZN.29, CO3.31 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:D.332, D:I.421, D:I.421 Hydrogen bonds: D:K.262, D:D.332 Water bridges: D:G.362 Salt bridges: D:K.262 ZED.41: 17 residues within 4Å: Chain E: K.250, D.255, K.262, M.270, D.273, N.330, D.332, A.333, E.334, R.336, L.360, T.361, G.362, I.421 Ligands: ZN.37, ZN.38, CO3.40 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:D.332, E:I.421, E:I.421 Hydrogen bonds: E:K.262, E:D.332 Water bridges: E:G.362 Salt bridges: E:K.262 ZED.50: 17 residues within 4Å: Chain F: K.250, D.255, K.262, M.270, D.273, N.330, D.332, A.333, E.334, R.336, L.360, T.361, G.362, I.421 Ligands: ZN.46, ZN.47, CO3.49 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:D.332, F:I.421, F:I.421 Hydrogen bonds: F:K.262, F:D.332 Water bridges: F:G.362 Salt bridges: F:K.262

24 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 6 residues within 4Å: Chain A: A.48, G.49, W.82, N.88, A.91, P.461 Ligand excluded by PLIP MPD.7: 9 residues within 4Å: Chain A: P.44, L.46, T.51, R.52 Chain D: Y.55, Q.99, D.102, L.103, E.104 Ligand excluded by PLIP MPD.8: 6 residues within 4Å: Chain A: L.133, N.176, E.177 Chain B: V.317, V.318, R.319 Ligand excluded by PLIP MPD.9: 8 residues within 4Å: Chain A: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.15: 6 residues within 4Å: Chain B: A.48, G.49, W.82, N.88, A.91, P.461 Ligand excluded by PLIP MPD.16: 9 residues within 4Å: Chain B: P.44, L.46, T.51, R.52 Chain F: Y.55, Q.99, D.102, L.103, E.104 Ligand excluded by PLIP MPD.17: 6 residues within 4Å: Chain B: L.133, N.176, E.177 Chain C: V.317, V.318, R.319 Ligand excluded by PLIP MPD.18: 8 residues within 4Å: Chain B: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.24: 6 residues within 4Å: Chain C: A.48, G.49, W.82, N.88, A.91, P.461 Ligand excluded by PLIP MPD.25: 9 residues within 4Å: Chain C: P.44, L.46, T.51, R.52 Chain E: Y.55, Q.99, D.102, L.103, E.104 Ligand excluded by PLIP MPD.26: 6 residues within 4Å: Chain A: V.317, V.318, R.319 Chain C: L.133, N.176, E.177 Ligand excluded by PLIP MPD.27: 8 residues within 4Å: Chain C: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.33: 6 residues within 4Å: Chain D: A.48, G.49, W.82, N.88, A.91, P.461 Ligand excluded by PLIP MPD.34: 9 residues within 4Å: Chain A: Y.55, Q.99, D.102, L.103, E.104 Chain D: P.44, L.46, T.51, R.52 Ligand excluded by PLIP MPD.35: 6 residues within 4Å: Chain D: L.133, N.176, E.177 Chain E: V.317, V.318, R.319 Ligand excluded by PLIP MPD.36: 8 residues within 4Å: Chain D: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.42: 6 residues within 4Å: Chain E: A.48, G.49, W.82, N.88, A.91, P.461 Ligand excluded by PLIP MPD.43: 9 residues within 4Å: Chain C: Y.55, Q.99, D.102, L.103, E.104 Chain E: P.44, L.46, T.51, R.52 Ligand excluded by PLIP MPD.44: 6 residues within 4Å: Chain E: L.133, N.176, E.177 Chain F: V.317, V.318, R.319 Ligand excluded by PLIP MPD.45: 8 residues within 4Å: Chain E: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.51: 6 residues within 4Å: Chain F: A.48, G.49, W.82, N.88, A.91, P.461 Ligand excluded by PLIP MPD.52: 9 residues within 4Å: Chain B: Y.55, Q.99, D.102, L.103, E.104 Chain F: P.44, L.46, T.51, R.52 Ligand excluded by PLIP MPD.53: 6 residues within 4Å: Chain D: V.317, V.318, R.319 Chain F: L.133, N.176, E.177 Ligand excluded by PLIP MPD.54: 8 residues within 4Å: Chain F: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cappiello, M. et al., Metal Ion Substitution in the Catalytic Site Greatly Affects the Binding of Sulfhydryl-Containing Compounds to Leucyl Aminopeptidase. Biochemistry (2006)

Release Date

2006-04-04

Peptides

Cytosol aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Cytosol aminopeptidase