SMTL ID : 1y0y.1

Crystal structure of tetrahedral aminopeptidase from P. horikoshii in complex with amastatin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-12-mer

Ligands

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

L2O-VAL-VAL-ASP.1: 16 residues within 4Å: Chain A: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.2, ZN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.216, A:L.293 Hydrogen bonds: A:D.182, A:D.235, A:V.236, A:G.297, A:G.297 Water bridges: A:I.322 Salt bridges: A:H.323 L2O-VAL-VAL-ASP.4: 16 residues within 4Å: Chain B: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.5, ZN.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.216, B:L.293 Hydrogen bonds: B:D.182, B:D.235, B:V.236, B:G.297, B:G.297 Water bridges: B:I.322 Salt bridges: B:H.323 L2O-VAL-VAL-ASP.7: 16 residues within 4Å: Chain C: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.8, ZN.9 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.216, C:L.293 Hydrogen bonds: C:D.182, C:D.182, C:D.235, C:V.236, C:G.297, C:G.297, C:I.322 Water bridges: C:E.213, C:I.322 Salt bridges: C:H.323 L2O-VAL-VAL-ASP.10: 16 residues within 4Å: Chain D: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.11, ZN.12 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.216, D:L.293 Hydrogen bonds: D:D.182, D:D.182, D:D.235, D:V.236, D:G.297, D:G.297, D:I.322 Water bridges: D:E.213, D:I.322 Salt bridges: D:H.323 L2O-VAL-VAL-ASP.13: 16 residues within 4Å: Chain E: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.14, ZN.15 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:L.216, E:L.293 Hydrogen bonds: E:D.182, E:D.235, E:V.236, E:G.297, E:G.297 Water bridges: E:I.322 Salt bridges: E:H.323 L2O-VAL-VAL-ASP.16: 16 residues within 4Å: Chain F: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.17, ZN.18 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:L.216, F:L.293 Hydrogen bonds: F:D.182, F:D.182, F:D.235, F:V.236, F:G.297, F:G.297, F:I.322 Water bridges: F:E.213, F:I.322 Salt bridges: F:H.323 L2O-VAL-VAL-ASP.19: 16 residues within 4Å: Chain G: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.20, ZN.21 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:L.216, G:L.293 Hydrogen bonds: G:D.182, G:D.235, G:V.236, G:G.297, G:G.297 Water bridges: G:I.322 Salt bridges: G:H.323 L2O-VAL-VAL-ASP.22: 16 residues within 4Å: Chain H: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.23, ZN.24 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:L.216, H:L.293 Hydrogen bonds: H:D.182, H:D.182, H:D.235, H:V.236, H:G.297, H:G.297, H:I.322 Water bridges: H:E.213, H:I.322 Salt bridges: H:H.323 L2O-VAL-VAL-ASP.25: 16 residues within 4Å: Chain I: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.26, ZN.27 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:L.216, I:L.293 Hydrogen bonds: I:D.182, I:D.182, I:D.235, I:V.236, I:G.297, I:G.297, I:I.322 Water bridges: I:I.322 Salt bridges: I:H.323 L2O-VAL-VAL-ASP.28: 16 residues within 4Å: Chain J: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.29, ZN.30 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:L.216, J:L.293 Hydrogen bonds: J:D.182, J:D.235, J:V.236, J:G.297, J:G.297 Water bridges: J:E.213, J:I.322 Salt bridges: J:H.323 L2O-VAL-VAL-ASP.31: 16 residues within 4Å: Chain K: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.32, ZN.33 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:L.216, K:L.293 Hydrogen bonds: K:D.182, K:D.235, K:V.236, K:G.297, K:G.297 Water bridges: K:E.213, K:I.322 Salt bridges: K:H.323 L2O-VAL-VAL-ASP.34: 16 residues within 4Å: Chain L: H.68, D.182, E.212, E.213, L.216, D.235, V.236, T.237, I.238, L.293, G.296, G.297, I.322, H.323 Ligands: ZN.35, ZN.36 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:L.216, L:L.293 Hydrogen bonds: L:D.182, L:D.182, L:D.235, L:V.236, L:G.297, L:G.297, L:I.322 Water bridges: L:I.322 Salt bridges: L:H.323

24 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.68, A:D.182, A:D.235, A:D.235 ZN.3: 6 residues within 4Å: Chain A: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.1, L2O-VAL-VAL-ASP.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.182, A:E.213, A:E.213, A:H.323 ZN.5: 6 residues within 4Å: Chain B: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.4, ZN.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.68, B:D.182, B:D.235, B:D.235 ZN.6: 6 residues within 4Å: Chain B: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.4, L2O-VAL-VAL-ASP.4, ZN.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.182, B:E.213, B:E.213, B:H.323 ZN.8: 6 residues within 4Å: Chain C: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.7, ZN.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.68, C:D.182, C:D.235, C:D.235 ZN.9: 6 residues within 4Å: Chain C: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.7, L2O-VAL-VAL-ASP.7, ZN.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.182, C:E.213, C:E.213, C:H.323 ZN.11: 6 residues within 4Å: Chain D: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.10, ZN.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.68, D:D.182, D:D.235, D:D.235 ZN.12: 6 residues within 4Å: Chain D: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.10, L2O-VAL-VAL-ASP.10, ZN.11 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.182, D:E.213, D:E.213, D:H.323 ZN.14: 6 residues within 4Å: Chain E: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.13, ZN.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.68, E:D.182, E:D.235, E:D.235 ZN.15: 6 residues within 4Å: Chain E: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.13, L2O-VAL-VAL-ASP.13, ZN.14 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.182, E:E.213, E:E.213, E:H.323 ZN.17: 6 residues within 4Å: Chain F: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.16, ZN.18 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.68, F:D.182, F:D.235, F:D.235 ZN.18: 6 residues within 4Å: Chain F: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.16, L2O-VAL-VAL-ASP.16, ZN.17 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.182, F:E.213, F:E.213, F:H.323 ZN.20: 6 residues within 4Å: Chain G: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.19, ZN.21 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.68, G:D.182, G:D.235, G:D.235 ZN.21: 6 residues within 4Å: Chain G: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.19, L2O-VAL-VAL-ASP.19, ZN.20 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.182, G:E.213, G:E.213, G:H.323 ZN.23: 6 residues within 4Å: Chain H: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.22, ZN.24 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.68, H:D.182, H:D.235, H:D.235 ZN.24: 6 residues within 4Å: Chain H: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.22, L2O-VAL-VAL-ASP.22, ZN.23 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.182, H:E.213, H:E.213, H:H.323 ZN.26: 6 residues within 4Å: Chain I: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.25, ZN.27 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.68, I:D.182, I:D.235, I:D.235 ZN.27: 6 residues within 4Å: Chain I: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.25, L2O-VAL-VAL-ASP.25, ZN.26 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.182, I:E.213, I:E.213, I:H.323 ZN.29: 6 residues within 4Å: Chain J: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.28, ZN.30 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.68, J:D.182, J:D.235, J:D.235 ZN.30: 6 residues within 4Å: Chain J: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.28, L2O-VAL-VAL-ASP.28, ZN.29 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.182, J:E.213, J:E.213, J:H.323 ZN.32: 6 residues within 4Å: Chain K: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.31, ZN.33 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.68, K:D.182, K:D.235, K:D.235 ZN.33: 6 residues within 4Å: Chain K: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.31, L2O-VAL-VAL-ASP.31, ZN.32 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.182, K:E.213, K:E.213, K:H.323 ZN.35: 6 residues within 4Å: Chain L: H.68, D.182, E.212, D.235 Ligands: L2O-VAL-VAL-ASP.34, ZN.36 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:H.68, L:D.182, L:D.235, L:D.235 ZN.36: 6 residues within 4Å: Chain L: D.182, E.213, H.323 Ligands: L2O-VAL-VAL-ASP.34, L2O-VAL-VAL-ASP.34, ZN.35 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.182, L:E.213, L:E.213, L:H.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borissenko, L. et al., Crystal Structure of TET Protease Reveals Complementary Protein Degradation Pathways in Prokaryotes. J.Mol.Biol. (2005)

Release Date

2005-03-01

Peptides

Frv operon protein FrvX: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Frv operon protein FrvX

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