SMTL ID : 3hws.1 (2 other biounits)

Crystal structure of nucleotide-bound hexameric ClpX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: Y.16, V.17, I.18, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, L.256, I.264, A.308 Ligands: SO4.9 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.18, A:G.61, A:S.62, A:S.62, A:G.63, A:K.64, A:T.65, A:T.65, A:L.66 Salt bridges: A:K.64 ADP.5: 17 residues within 4Å: Chain B: Y.16, V.17, I.18, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, L.256, I.264, A.308, R.309 Ligands: SO4.8, MG.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:I.18, B:P.59, B:G.61, B:S.62, B:S.62, B:G.63, B:K.64, B:T.65, B:T.65, B:L.66 Salt bridges: B:K.64, B:R.309, B:R.309 ADP.15: 14 residues within 4Å: Chain D: Y.16, V.17, I.18, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, I.264, A.308, R.309 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:I.18, D:G.61, D:S.62, D:S.62, D:G.63, D:K.64, D:T.65, D:T.65, D:T.65, D:L.66 Salt bridges: D:K.64, D:R.309, D:R.309 ADP.18: 16 residues within 4Å: Chain E: Y.16, V.17, I.18, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, L.256, I.264, P.268, A.308, R.309 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:I.18, E:I.18, E:G.61, E:S.62, E:G.63, E:K.64, E:T.65, E:L.66, E:R.309 Salt bridges: E:K.64

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.10, K.25 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.10, A:K.25 SO4.3: 4 residues within 4Å: Chain A: F.79, T.80, M.81, K.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.80, A:M.81 Salt bridges: A:K.107 SO4.4: 5 residues within 4Å: Chain A: G.19, Q.20, E.21, Q.22, N.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.20, A:E.21, A:Q.22, A:N.254 SO4.6: 5 residues within 4Å: Chain B: G.19, Q.20, E.21, Q.22, N.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.20, B:E.21, B:Q.22, B:N.254 SO4.7: 3 residues within 4Å: Chain B: G.41, D.42, T.43 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.42, B:T.43 SO4.8: 2 residues within 4Å: Ligands: ADP.5, MG.10 No protein-ligand interaction detected (PLIP) SO4.9: 1 residues within 4Å: Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.246 SO4.11: 8 residues within 4Å: Chain C: P.59, T.60, G.61, S.62, G.63, K.64, T.65, Y.121 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.61, C:S.62, C:S.62, C:G.63, C:K.64, C:T.65, C:Y.121 Salt bridges: C:K.64 SO4.12: 3 residues within 4Å: Chain C: T.80, M.81, K.107 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.80, C:M.81 Salt bridges: C:K.103, C:K.107 SO4.13: 2 residues within 4Å: Chain C: K.300, R.304 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.300, C:R.304 SO4.14: 4 residues within 4Å: Chain C: G.19, Q.20, E.21, N.254 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.20, C:E.21, C:N.254 SO4.16: 2 residues within 4Å: Chain D: H.7, N.11 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.11, C:S.328 Salt bridges: D:H.7 SO4.19: 7 residues within 4Å: Chain F: P.59, T.60, G.61, S.62, G.63, K.64, T.65 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.61, F:S.62, F:S.62, F:G.63, F:K.64, F:T.65 Salt bridges: F:K.64

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain B: A.308, R.309 Ligands: ADP.5, SO4.8 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain D: V.201, D.233 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glynn, S.E. et al., Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Cell(Cambridge,Mass.) (2009)

Release Date

2009-11-24

Peptides

ATP-dependent Clp protease ATP-binding subunit clpX: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATP-dependent Clp protease ATP-binding subunit clpX

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