SMTL ID : 4ypm.1

Crystal structure of a LonA protease domain in complex with bortezomib

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

6 x BO2: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE(Covalent)

BO2.1: 18 residues within 4Å: Chain A: L.110, A.111, W.112, T.113, T.118, L.120, M.143, T.182, P.183, K.184, D.185, G.186, P.187, S.188, A.189, K.231 Ligands: MG.2, PEG.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.120, A:A.189 Hydrogen bonds: A:W.112, A:W.112, A:D.185, A:D.185, A:S.188, A:K.231 BO2.5: 18 residues within 4Å: Chain B: L.110, A.111, W.112, T.113, T.118, L.120, M.143, T.182, P.183, K.184, D.185, G.186, P.187, S.188, A.189, K.231 Ligands: MG.6, PEG.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.120, B:A.189 Hydrogen bonds: B:W.112, B:W.112, B:D.185, B:D.185, B:S.188, B:K.231 BO2.9: 18 residues within 4Å: Chain C: L.110, A.111, W.112, T.113, T.118, L.120, M.143, T.182, P.183, K.184, D.185, G.186, P.187, S.188, A.189, K.231 Ligands: MG.10, PEG.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.120, C:A.189 Hydrogen bonds: C:W.112, C:W.112, C:D.185, C:D.185, C:S.188, C:K.231 BO2.13: 18 residues within 4Å: Chain D: L.110, A.111, W.112, T.113, T.118, L.120, M.143, T.182, P.183, K.184, D.185, G.186, P.187, S.188, A.189, K.231 Ligands: MG.14, PEG.15 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.120, D:A.189 Hydrogen bonds: D:W.112, D:W.112, D:D.185, D:D.185, D:S.188, D:K.231 BO2.17: 18 residues within 4Å: Chain E: L.110, A.111, W.112, T.113, T.118, L.120, M.143, T.182, P.183, K.184, D.185, G.186, P.187, S.188, A.189, K.231 Ligands: MG.18, PEG.19 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.120, E:A.189 Hydrogen bonds: E:W.112, E:W.112, E:D.185, E:D.185, E:S.188, E:K.231 BO2.21: 18 residues within 4Å: Chain F: L.110, A.111, W.112, T.113, T.118, L.120, M.143, T.182, P.183, K.184, D.185, G.186, P.187, S.188, A.189, K.231 Ligands: MG.22, PEG.23 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:L.120, F:A.189 Hydrogen bonds: F:W.112, F:W.112, F:D.185, F:D.185, F:S.188, F:K.231

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: L.110, S.188, A.189, T.213, K.231 Ligands: BO2.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.110, A:S.188, A:S.188, A:T.213, H2O.4 MG.6: 6 residues within 4Å: Chain B: L.110, S.188, A.189, T.213, K.231 Ligands: BO2.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.110, B:S.188, B:S.188, B:T.213, H2O.14 MG.10: 6 residues within 4Å: Chain C: L.110, S.188, A.189, T.213, K.231 Ligands: BO2.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:L.110, C:S.188, C:S.188, C:T.213, H2O.23 MG.14: 6 residues within 4Å: Chain D: L.110, S.188, A.189, T.213, K.231 Ligands: BO2.13 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.110, D:S.188, D:S.188, D:T.213, H2O.33 MG.18: 6 residues within 4Å: Chain E: L.110, S.188, A.189, T.213, K.231 Ligands: BO2.17 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:L.110, E:S.188, E:S.188, E:T.213, H2O.43 MG.22: 6 residues within 4Å: Chain F: L.110, S.188, A.189, T.213, K.231 Ligands: BO2.21 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:L.110, F:S.188, F:S.188, F:T.213, H2O.52

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: W.112, T.113, P.114 Ligands: BO2.1 No protein-ligand interaction detected (PLIP) PEG.7: 4 residues within 4Å: Chain B: W.112, T.113, P.114 Ligands: BO2.5 No protein-ligand interaction detected (PLIP) PEG.11: 4 residues within 4Å: Chain C: W.112, T.113, P.114 Ligands: BO2.9 No protein-ligand interaction detected (PLIP) PEG.15: 4 residues within 4Å: Chain D: W.112, T.113, P.114 Ligands: BO2.13 No protein-ligand interaction detected (PLIP) PEG.19: 4 residues within 4Å: Chain E: W.112, T.113, P.114 Ligands: BO2.17 No protein-ligand interaction detected (PLIP) PEG.23: 4 residues within 4Å: Chain F: W.112, T.113, P.114 Ligands: BO2.21 No protein-ligand interaction detected (PLIP)

6 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 4 residues within 4Å: Chain A: I.90, R.207, K.242, E.265 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.90 Water bridges: A:K.242, A:K.242, A:Y.278 Salt bridges: A:R.207, A:K.242, A:K.242 CIT.8: 4 residues within 4Å: Chain B: I.90, R.207, K.242, E.265 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.90 Water bridges: B:K.242, B:K.242, B:Y.278 Salt bridges: B:R.207, B:K.242, B:K.242 CIT.12: 4 residues within 4Å: Chain C: I.90, R.207, K.242, E.265 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.90 Water bridges: C:K.242, C:K.242, C:Y.278 Salt bridges: C:R.207, C:K.242, C:K.242 CIT.16: 4 residues within 4Å: Chain D: I.90, R.207, K.242, E.265 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.90 Water bridges: D:K.242, D:K.242, D:Y.278 Salt bridges: D:R.207, D:K.242, D:K.242 CIT.20: 4 residues within 4Å: Chain E: I.90, R.207, K.242, E.265 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.90 Water bridges: E:K.242, E:K.242, E:Y.278 Salt bridges: E:R.207, E:K.242, E:K.242 CIT.24: 4 residues within 4Å: Chain F: I.90, R.207, K.242, E.265 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:I.90 Water bridges: F:K.242, F:K.242, F:Y.278 Salt bridges: F:R.207, F:K.242, F:K.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, S.-C. et al., Structural Basis for the Magnesium-Dependent Activation and Hexamerization 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
A

C
A

D
A

E
A

F
A

Lon protease