6P4W

XPB helicase in a complex with truncated Bax1 from Sulfurisphaera tokodaii at 2.96 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6P4W/pdb

Classification: HYDROLASE/DNA BINDING PROTEIN
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-28 Released: 2020-06-03
Deposition Author(s): Fan, L., He, F., DuPrez, K.T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free: 0.233
R-Value Work: 0.183
R-Value Observed: 0.185

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

XPB helicase in a complex with truncated Bax1 from Sulfurisphaera tokodaii at 2.96 Angstrom resolution

Fan, L., He, F., DuPrez, K.T.

To be published.

Macromolecule Content

Total Structure Weight: 191.39 kDa
Atom Count: 13,068
Modelled Residue Count: 1,617
Deposited Residue Count: 1,628
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-dependent ATPase XPBII	A, C	440	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: xpb2, ST1613, STK_16130 EC: 5.6.2.4
UniProt
Find proteins for Q970I2 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970I2 Go to UniProtKB: Q970I2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q970I2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease Bax1	B, D	374	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: bax1, ST1614, STK_16140 EC: 3.1
UniProt
Find proteins for Q970I1 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970I1 Go to UniProtKB: Q970I1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q970I1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain R [auth C] mmCIF format, chain E [auth A] mmCIF format, chain R [auth C]	E [auth A], R [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain R [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth C] MOL2 format, chain G [auth A] MOL2 format, chain T [auth C] mmCIF format, chain G [auth A] mmCIF format, chain T [auth C]	G [auth A], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain T [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth D] H [auth A] I [auth A] J [auth A] AA [auth C], BA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth B], Q [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain S [auth C] mmCIF format, chain F [auth A] mmCIF format, chain S [auth C]	F [auth A], S [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain S [auth C]