SMTL ID : 5tnu.1 (1 other biounit)

S. tokodaii XPB II crystal structure at 3.0 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

monomer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: T.112, G.113, A.114, G.115, K.116, T.117 Ligands: SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.113, A:A.114, A:G.115, A:K.116 Salt bridges: A:K.116 SO4.2: 7 residues within 4Å: Chain A: G.115, T.117, Q.118, R.147, Y.151 Ligands: SO4.1, CL.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.115, A:T.117, A:Q.118, A:Q.118, A:Y.151 Salt bridges: A:R.147 SO4.3: 1 residues within 4Å: Chain A: R.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.118 Salt bridges: A:R.90 SO4.4: 3 residues within 4Å: Chain A: K.84, K.86, D.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.153 Salt bridges: A:K.84, A:K.86 SO4.5: 4 residues within 4Å: Chain A: G.160, G.161, G.162, E.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.160, A:G.162, A:S.176 SO4.6: 6 residues within 4Å: Chain A: R.278, W.318, L.322, A.449, R.452, R.456 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.278, A:R.452, A:R.456 SO4.7: 4 residues within 4Å: Chain A: Y.274, R.278, G.447, R.452 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.274 Salt bridges: A:R.278, A:R.452

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: T.137, I.138 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.147, K.150, Y.151 Ligands: SO4.2 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.456 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: S.201, R.225 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: S.201, E.202 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: L.82, I.83, K.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.83, A:I.83 GOL.14: 3 residues within 4Å: Chain A: D.85, S.125, K.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.125, A:K.128 GOL.15: 3 residues within 4Å: Chain A: Y.36, P.38, G.39 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.36, A:Y.36, A:G.39 GOL.16: 3 residues within 4Å: Chain A: Y.257, K.258, I.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.255, A:I.259, A:I.259 GOL.17: 4 residues within 4Å: Chain A: N.149, D.153, F.154, D.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.149 Water bridges: A:D.155 GOL.18: 3 residues within 4Å: Chain A: R.57, K.61, E.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.57, A:R.57, A:E.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kahanda, D. et al., Application of Electrochemical Devices to Characterize the Dynamic Actions of Helicases on DNA. Anal.Chem. (2018)

Release Date

2017-11-01

Peptides

DNA-dependent ATPase XPBII: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-dependent ATPase XPBII

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