SMTL ID : 6h7x.1

First X-ray structure of full-length human RuvB-Like 2.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-hexamer

Ligands

18 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.305, R.336 Ligands: PEG.5 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: S.398, R.400, Y.401, D.435, E.436 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: Q.49, T.360, P.361, D.366 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: D.305, R.336 Ligands: PEG.16 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain B: S.398, R.400, Y.401, D.435, E.436 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain B: Q.49, T.360, P.361, D.366 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain C: D.305, R.336 Ligands: PEG.27 No protein-ligand interaction detected (PLIP) MG.24: 5 residues within 4Å: Chain C: S.398, R.400, Y.401, D.435, E.436 No protein-ligand interaction detected (PLIP) MG.25: 4 residues within 4Å: Chain C: Q.49, T.360, P.361, D.366 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain D: D.305, R.336 Ligands: PEG.38 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain D: S.398, R.400, Y.401, D.435, E.436 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain D: Q.49, T.360, P.361, D.366 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain E: D.305, R.336 Ligands: PEG.49 No protein-ligand interaction detected (PLIP) MG.46: 5 residues within 4Å: Chain E: S.398, R.400, Y.401, D.435, E.436 No protein-ligand interaction detected (PLIP) MG.47: 4 residues within 4Å: Chain E: Q.49, T.360, P.361, D.366 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain F: D.305, R.336 Ligands: PEG.60 No protein-ligand interaction detected (PLIP) MG.57: 5 residues within 4Å: Chain F: S.398, R.400, Y.401, D.435, E.436 No protein-ligand interaction detected (PLIP) MG.58: 4 residues within 4Å: Chain F: Q.49, T.360, P.361, D.366 No protein-ligand interaction detected (PLIP)

42 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: S.431, L.432, L.434 Chain E: V.357, S.358 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: G.77, K.83, D.299, E.300, T.328, N.329 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: T.440, Q.441, Y.442, M.443, K.444 Chain E: G.331 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: G.89, Q.92 Ligands: EDO.9 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: Q.44, R.53 Ligands: EDO.8 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: P.79, G.80, T.81, G.82, K.83, T.84 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: V.380, E.381, S.410, C.413, R.414, T.419 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: S.431, L.432, L.434 Chain F: V.357, S.358 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: G.77, K.83, D.299, E.300, T.328, N.329 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: T.440, Q.441, Y.442, M.443, K.444 Chain F: G.331 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: G.89, Q.92 Ligands: EDO.20 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: Q.44, R.53 Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: P.79, G.80, T.81, G.82, K.83, T.84 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: V.380, E.381, S.410, C.413, R.414, T.419 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: S.431, L.432, L.434 Chain D: V.357, S.358 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain C: G.77, K.83, D.299, E.300, T.328, N.329 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain C: T.440, Q.441, Y.442, M.443, K.444 Chain D: G.331 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain C: G.89, Q.92 Ligands: EDO.31 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: Q.44, R.53 Ligands: EDO.30 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: P.79, G.80, T.81, G.82, K.83, T.84 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: V.380, E.381, S.410, C.413, R.414, T.419 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain B: V.357, S.358 Chain D: S.431, L.432, L.434 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain D: G.77, K.83, D.299, E.300, T.328, N.329 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain B: G.331 Chain D: T.440, Q.441, Y.442, M.443, K.444 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain D: G.89, Q.92 Ligands: EDO.42 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain D: Q.44, R.53 Ligands: EDO.41 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain D: P.79, G.80, T.81, G.82, K.83, T.84 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain D: V.380, E.381, S.410, C.413, R.414, T.419 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain C: V.357, S.358 Chain E: S.431, L.432, L.434 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain E: G.77, K.83, D.299, E.300, T.328, N.329 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain C: G.331 Chain E: T.440, Q.441, Y.442, M.443, K.444 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain E: G.89, Q.92 Ligands: EDO.53 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain E: Q.44, R.53 Ligands: EDO.52 Ligand excluded by PLIP EDO.54: 6 residues within 4Å: Chain E: P.79, G.80, T.81, G.82, K.83, T.84 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain E: V.380, E.381, S.410, C.413, R.414, T.419 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain A: V.357, S.358 Chain F: S.431, L.432, L.434 Ligand excluded by PLIP EDO.61: 6 residues within 4Å: Chain F: G.77, K.83, D.299, E.300, T.328, N.329 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain A: G.331 Chain F: T.440, Q.441, Y.442, M.443, K.444 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain F: G.89, Q.92 Ligands: EDO.64 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain F: Q.44, R.53 Ligands: EDO.63 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain F: P.79, G.80, T.81, G.82, K.83, T.84 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain F: V.380, E.381, S.410, C.413, R.414, T.419 Ligand excluded by PLIP

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

PEG.5: 6 residues within 4Å: Chain A: K.115, D.305, I.306, E.307, G.337 Ligands: MG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.305, A:E.307 PEG.16: 6 residues within 4Å: Chain B: K.115, D.305, I.306, E.307, G.337 Ligands: MG.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.305, B:E.307 PEG.27: 6 residues within 4Å: Chain C: K.115, D.305, I.306, E.307, G.337 Ligands: MG.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.305, C:E.307 PEG.38: 6 residues within 4Å: Chain D: K.115, D.305, I.306, E.307, G.337 Ligands: MG.34 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.305, D:E.307 PEG.49: 6 residues within 4Å: Chain E: K.115, D.305, I.306, E.307, G.337 Ligands: MG.45 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.305, E:E.307 PEG.60: 6 residues within 4Å: Chain F: K.115, D.305, I.306, E.307, G.337 Ligands: MG.56 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.305, F:E.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva, S.T.N. et al., X-ray structure of full-length human RuvB-Like 2 - mechanistic insights into coupling between ATP binding and mechanical action. Sci Rep (2018)

Release Date

2018-08-08

Peptides

RuvB-like 2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

RuvB-like 2

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