6P4O | pdb_00006p4o

Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution

PDB DOI: https://doi.org/10.2210/pdb6P4O/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., 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: 3.15 Å
R-Value Free:
0.282 (Depositor), 0.280 (DCC)
R-Value Work:
0.265 (Depositor), 0.270 (DCC)
R-Value Observed:
0.266 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution

Fan, L., DuPrez, K.T.

To be published.

Macromolecule Content

Total Structure Weight: 336.45 kDa
Atom Count: 20,038
Modelled Residue Count: 2,753
Deposited Residue Count: 2,880
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-dependent ATPase XPBII	A, C, E	459	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 LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease Bax1	B, D, F	501	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 LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth E] MOL2 format, chain G [auth A] MOL2 format, chain L [auth E] mmCIF format, chain G [auth A] mmCIF format, chain L [auth E]	G [auth A], L [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth E] Interactions & Density Focus chain G [auth A] Focus chain L [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth F] SDF format, chain N [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F]	H [auth A], I [auth A], J [auth A], M [auth F], N [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth F] Focus chain N [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth F] Focus chain N [auth F]