SMTL ID : 4ypl.1

Crystal structure of a hexameric LonA protease bound to three ADPs

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

homo-hexamer

Ligands

6 x 4KZ: N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide(Covalent)

4KZ.1: 15 residues within 4Å: Chain A: L.362, A.363, W.364, L.372, I.374, M.395, V.429, P.435, K.436, D.437, G.438, P.439, S.440, A.441, K.483 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.363, A:L.372, A:I.374, A:V.429, A:A.441 Hydrogen bonds: A:W.364, A:W.364, A:D.437, A:D.437, A:G.438, A:S.440, A:A.441, A:K.483 4KZ.3: 14 residues within 4Å: Chain B: L.362, A.363, W.364, T.365, T.370, L.372, M.395, K.436, D.437, G.438, P.439, S.440, A.441, K.483 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.363, B:A.441 Hydrogen bonds: B:W.364, B:D.437, B:D.437, B:S.440, B:K.483 4KZ.4: 15 residues within 4Å: Chain C: L.362, A.363, W.364, T.365, T.370, L.372, M.395, P.435, K.436, D.437, G.438, P.439, S.440, A.441, K.483 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:A.363, C:L.372, C:A.441 Hydrogen bonds: C:W.364, C:W.364, C:D.437, C:D.437, C:D.437, C:S.440, C:K.483 4KZ.6: 15 residues within 4Å: Chain D: L.362, A.363, W.364, T.365, T.370, M.395, T.434, P.435, K.436, D.437, G.438, P.439, S.440, A.441, K.483 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.363, D:K.436, D:A.441 Hydrogen bonds: D:W.364, D:W.364, D:D.437, D:D.437, D:S.440, D:K.483 4KZ.8: 14 residues within 4Å: Chain E: A.363, W.364, T.365, T.370, L.372, M.395, P.435, K.436, D.437, G.438, P.439, S.440, A.441, K.483 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:A.363, E:L.372, E:A.441 Hydrogen bonds: E:W.364, E:W.364, E:D.437, E:S.440, E:K.483 4KZ.9: 14 residues within 4Å: Chain F: L.362, A.363, W.364, T.365, T.370, M.395, T.434, P.435, K.436, D.437, G.438, P.439, S.440, K.483 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.363, F:W.364 Hydrogen bonds: F:W.364, F:W.364, F:D.437, F:S.440, F:K.483

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

ADP.2: 19 residues within 4Å: Chain B: D.80, H.81, Y.82, L.84, P.119, G.120, V.121, G.122, K.123, T.124, S.125, Y.255, I.263, Y.267, L.268, K.271, V.302, R.303, E.306 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:H.81, B:Y.82, B:P.118, B:G.120, B:V.121, B:G.122, B:K.123, B:T.124, B:S.125, B:S.125, B:S.125, B:Y.255, B:Y.255, B:K.271 Salt bridges: B:K.123, B:R.303, B:R.303 pi-Stacking: B:H.81 ADP.5: 20 residues within 4Å: Chain D: D.80, H.81, Y.82, L.84, P.118, P.119, G.120, V.121, G.122, K.123, T.124, S.125, Y.255, I.263, Y.267, L.268, K.271, V.302, R.303, E.306 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Y.82, D:Y.82, D:G.120, D:V.121, D:G.122, D:K.123, D:T.124, D:T.124, D:T.124, D:S.125, D:Y.255, D:K.271, D:E.306 Salt bridges: D:K.123, D:R.303, D:R.303 pi-Stacking: D:H.81 ADP.7: 15 residues within 4Å: Chain E: H.81, Y.82, L.84, G.120, V.121, G.122, K.123, T.124, S.125, Y.255, I.263, Y.267, V.302, R.303, E.306 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:Y.82, E:G.120, E:V.121, E:G.122, E:K.123, E:T.124, E:T.124, E:S.125, E:Y.255, E:R.303, E:E.306 Salt bridges: E:K.123 pi-Stacking: E:H.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, C.-C. et al., Structural Insights into the Allosteric Operation of the Lon AAA+ Protease. Structure (2016)

Release Date

2016-03-16

Peptides

Lon protease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
D

F
E

Lon protease