SMTL ID : 1n6d.1

Tricorn protease in complex with tetrapeptide chloromethyl ketone derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x ARG- VAL- ARG- LYS: RVRK(Non-covalent)

ARG-VAL-ARG-LYS.1: 18 residues within 4Å: Chain A: E.605, Y.609, H.746, G.917, G.918, F.919, S.965, D.966, I.969, G.993, I.994, T.995, F.1011, F.1013 Chain B: F.531, D.936 Ligands: D10.7, CHM.8 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.969, A:F.1011, A:F.1011 Hydrogen bonds: A:Y.609, A:Y.609, A:G.918, A:G.918, A:D.966, A:I.994, A:I.994, A:T.995, B:D.936 Salt bridges: A:E.605 pi-Cation interactions: A:Y.609 ARG-VAL-ARG-LYS.2: 18 residues within 4Å: Chain A: F.531, D.936 Chain B: E.605, Y.609, H.746, G.917, G.918, F.919, S.965, D.966, I.969, G.993, I.994, T.995, F.1011, F.1013 Ligands: D10.9, CHM.10 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.969, B:F.1011, B:F.1011 Hydrogen bonds: B:Y.609, B:Y.609, B:G.918, B:G.918, B:D.966, B:I.994, B:I.994, B:T.995, A:D.936 Salt bridges: B:E.605 pi-Cation interactions: B:Y.609 ARG-VAL-ARG-LYS.3: 18 residues within 4Å: Chain C: E.605, Y.609, H.746, G.917, G.918, F.919, S.965, D.966, I.969, G.993, I.994, T.995, F.1011, F.1013 Chain D: F.531, D.936 Ligands: D10.11, CHM.12 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.969, C:F.1011, C:F.1011 Hydrogen bonds: C:Y.609, C:Y.609, C:G.918, C:G.918, C:D.966, C:I.994, C:I.994, C:T.995, C:T.995, D:D.936 Salt bridges: C:E.605 pi-Cation interactions: C:Y.609 ARG-VAL-ARG-LYS.4: 18 residues within 4Å: Chain C: F.531, D.936 Chain D: E.605, Y.609, H.746, G.917, G.918, F.919, S.965, D.966, I.969, G.993, I.994, T.995, F.1011, F.1013 Ligands: D10.13, CHM.14 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.969, D:F.1011, D:F.1011 Hydrogen bonds: D:Y.609, D:Y.609, D:G.918, D:G.918, D:D.966, D:I.994, D:I.994, D:T.995, C:D.936 Salt bridges: D:E.605 pi-Cation interactions: D:Y.609 ARG-VAL-ARG-LYS.5: 18 residues within 4Å: Chain E: E.605, Y.609, H.746, G.917, G.918, F.919, S.965, D.966, I.969, G.993, I.994, T.995, F.1011, F.1013 Chain F: F.531, D.936 Ligands: D10.15, CHM.16 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:I.969, E:F.1011, E:F.1011 Hydrogen bonds: E:Y.609, E:Y.609, E:G.918, E:G.918, E:D.966, E:I.994, E:I.994, E:T.995, F:D.936 Salt bridges: E:E.605 pi-Cation interactions: E:Y.609 ARG-VAL-ARG-LYS.6: 18 residues within 4Å: Chain E: F.531, D.936 Chain F: E.605, Y.609, H.746, G.917, G.918, F.919, S.965, D.966, I.969, G.993, I.994, T.995, F.1011, F.1013 Ligands: D10.17, CHM.18 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:I.969, F:F.1011, F:F.1011 Hydrogen bonds: F:Y.609, F:Y.609, F:G.918, F:G.918, F:D.966, F:I.994, F:I.994, F:T.995, F:T.995, E:D.936 Water bridges: F:S.965 Salt bridges: F:E.605 pi-Cation interactions: F:Y.609

6 x D10: DECANE(Non-covalent)

D10.7: 5 residues within 4Å: Chain A: F.408, T.995, P.996, K.997 Ligands: ARG-VAL-ARG-LYS.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.408, A:K.997 D10.9: 5 residues within 4Å: Chain B: F.408, T.995, P.996, K.997 Ligands: ARG-VAL-ARG-LYS.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.408, B:K.997 D10.11: 5 residues within 4Å: Chain C: F.408, T.995, P.996, K.997 Ligands: ARG-VAL-ARG-LYS.3 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.408, C:K.997 D10.13: 4 residues within 4Å: Chain D: T.995, P.996, K.997 Ligands: ARG-VAL-ARG-LYS.4 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.997 D10.15: 4 residues within 4Å: Chain E: T.995, P.996, K.997 Ligands: ARG-VAL-ARG-LYS.5 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:K.997 D10.17: 5 residues within 4Å: Chain F: F.408, T.995, P.996, K.997 Ligands: ARG-VAL-ARG-LYS.6 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.408, F:K.997

6 x CHM: 1,3-DICHLORO-PROPAN-2-ONE(Covalent)

CHM.8: 4 residues within 4Å: Chain A: H.746, S.965, G.990 Ligands: ARG-VAL-ARG-LYS.1 No protein-ligand interaction detected (PLIP) CHM.10: 4 residues within 4Å: Chain B: H.746, S.965, G.990 Ligands: ARG-VAL-ARG-LYS.2 No protein-ligand interaction detected (PLIP) CHM.12: 4 residues within 4Å: Chain C: H.746, S.965, G.990 Ligands: ARG-VAL-ARG-LYS.3 No protein-ligand interaction detected (PLIP) CHM.14: 4 residues within 4Å: Chain D: H.746, S.965, G.990 Ligands: ARG-VAL-ARG-LYS.4 No protein-ligand interaction detected (PLIP) CHM.16: 4 residues within 4Å: Chain E: H.746, S.965, G.990 Ligands: ARG-VAL-ARG-LYS.5 No protein-ligand interaction detected (PLIP) CHM.18: 4 residues within 4Å: Chain F: H.746, S.965, G.990 Ligands: ARG-VAL-ARG-LYS.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.-S. et al., Navigation Inside a Protease: Substrate Selection and Product Exit in the Tricorn Proteasefrom Thermoplasma acidophilum. J.Mol.Biol. (2002)

Release Date

2002-12-30

Peptides

tricorn protease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

tricorn protease

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