SMTL ID : 3k1j.1

Crystal structure of Lon protease from Thermococcus onnurineus NA1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: Q.42, V.43, I.44, E.68, P.69, G.70, T.71, G.72, K.73, S.74, M.75, F.301, Q.304, E.305, R.308, L.341, R.342 Chain D: Y.278 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:I.44, A:I.44, A:G.70, A:T.71, A:G.72, A:K.73, A:S.74, A:M.75, A:R.308, D:Y.278 Water bridges: A:Q.46, A:K.73, A:D.208, A:D.208, A:R.308, A:R.308, A:R.342 Salt bridges: A:K.73 ADP.4: 15 residues within 4Å: Chain B: V.43, I.44, Q.46, E.68, P.69, G.70, T.71, G.72, K.73, S.74, M.75, E.305, R.308, L.341, R.342 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:I.44, B:G.70, B:T.71, B:T.71, B:T.71, B:G.72, B:K.73, B:S.74, B:M.75, B:R.308, B:R.308, B:R.342 Water bridges: B:K.73, B:D.208, B:D.208 Salt bridges: B:K.73 ADP.5: 18 residues within 4Å: Chain C: Q.42, V.43, I.44, E.68, P.69, G.70, T.71, G.72, K.73, S.74, M.75, F.301, Q.304, E.305, R.308, L.341, R.342 Chain F: Y.278 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:I.44, C:I.44, C:G.70, C:T.71, C:G.72, C:K.73, C:S.74, C:M.75, C:R.308, F:Y.278 Water bridges: C:Q.46, C:K.73, C:D.208, C:D.208, C:R.308, C:R.308, C:R.342 Salt bridges: C:K.73 ADP.8: 15 residues within 4Å: Chain D: V.43, I.44, Q.46, E.68, P.69, G.70, T.71, G.72, K.73, S.74, M.75, E.305, R.308, L.341, R.342 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:I.44, D:G.70, D:T.71, D:T.71, D:T.71, D:G.72, D:K.73, D:S.74, D:M.75, D:R.308, D:R.308, D:R.342 Water bridges: D:K.73, D:D.208, D:D.208 Salt bridges: D:K.73 ADP.9: 18 residues within 4Å: Chain B: Y.278 Chain E: Q.42, V.43, I.44, E.68, P.69, G.70, T.71, G.72, K.73, S.74, M.75, F.301, Q.304, E.305, R.308, L.341, R.342 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:I.44, E:I.44, E:G.70, E:T.71, E:G.72, E:K.73, E:S.74, E:M.75, E:R.308, B:Y.278 Water bridges: E:Q.46, E:K.73, E:D.208, E:D.208, E:R.308, E:R.308, E:R.342 Salt bridges: E:K.73 ADP.12: 15 residues within 4Å: Chain F: V.43, I.44, Q.46, E.68, P.69, G.70, T.71, G.72, K.73, S.74, M.75, E.305, R.308, L.341, R.342 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:I.44, F:G.70, F:T.71, F:T.71, F:T.71, F:G.72, F:K.73, F:S.74, F:M.75, F:R.308, F:R.308, F:R.342 Water bridges: F:K.73, F:D.208, F:D.208 Salt bridges: F:K.73

3 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.2: 11 residues within 4Å: Chain A: Y.386, K.390, Y.393, I.418, L.420, L.476, Q.477, T.478, Y.479, E.480, G.481 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.390, A:E.480 Water bridges: A:Y.479 PE8.6: 11 residues within 4Å: Chain C: Y.386, K.390, Y.393, I.418, L.420, L.476, Q.477, T.478, Y.479, E.480, G.481 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.390, C:E.480 Water bridges: C:Y.479 PE8.10: 11 residues within 4Å: Chain E: Y.386, K.390, Y.393, I.418, L.420, L.476, Q.477, T.478, Y.479, E.480, G.481 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.390, E:E.480 Water bridges: E:Y.479

3 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.3: 5 residues within 4Å: Chain A: Y.393, Y.479 Chain D: P.522, I.523, G.524 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.332 PE4.7: 5 residues within 4Å: Chain C: Y.393, Y.479 Chain F: P.522, I.523, G.524 1 PLIP interactions: 1 interactions with chain F Water bridges: F:G.332 PE4.11: 5 residues within 4Å: Chain B: P.522, I.523, G.524 Chain E: Y.393, Y.479 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cha, S.S. et al., Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber. Embo J. (2010)

Release Date

2010-09-22

Peptides

ATP-dependent protease Lon: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

ATP-dependent protease Lon