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

Crystal structure of nucleotide-bound hexameric ClpX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-trimer

Ligands

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

ADP.1: 17 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, R.309 Ligands: SO4.4, MG.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:I.18, A:P.59, 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, A:R.309, A:R.309 ADP.11: 14 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:I.18, C:G.61, C:S.62, C:S.62, C:G.63, C:K.64, C:T.65, C:T.65, C:T.65, C:L.66 Salt bridges: C:K.64, C:R.309, C:R.309

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

SO4.2: 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 SO4.3: 3 residues within 4Å: Chain A: G.41, D.42, T.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.42, A:T.43 SO4.4: 2 residues within 4Å: Ligands: ADP.1, MG.6 No protein-ligand interaction detected (PLIP) SO4.5: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.246 SO4.7: 8 residues within 4Å: Chain B: P.59, T.60, G.61, S.62, G.63, K.64, T.65, Y.121 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.61, B:S.62, B:S.62, B:G.63, B:K.64, B:T.65, B:Y.121 Salt bridges: B:K.64 SO4.8: 3 residues within 4Å: Chain B: T.80, M.81, K.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.80, B:M.81 Salt bridges: B:K.103, B:K.107 SO4.9: 2 residues within 4Å: Chain B: K.300, R.304 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.300, B:R.304 SO4.10: 4 residues within 4Å: Chain B: G.19, Q.20, E.21, N.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.20, B:E.21, B:N.254 SO4.12: 2 residues within 4Å: Chain C: H.7, N.11 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.11, B:S.328 Salt bridges: C:H.7

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: A.308, R.309 Ligands: ADP.1, SO4.4 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain C: V.201, D.233 1 PLIP interactions: 1 interactions with chain C Metal complexes: C: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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

ATP-dependent Clp protease ATP-binding subunit clpX

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