8DK9 | pdb_00008dk9

Sliding-clamp-DinX peptide

PDB DOI: https://doi.org/10.2210/pdb8DK9/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Mycolicibacterium thermoresistibile, Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-05 Released: 2023-01-18
Deposition Author(s): Kapur, M.K., Gray, O.J., Honzatko, R.H., Nelson, S.N.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Interaction of sliding clamp with mycobacterial polymerases

Kapur, M.K., Gray, O.J., Honzatko, R.H., Nelson, S.N.

To be published.

Macromolecule Content

Total Structure Weight: 170.14 kDa
Atom Count: 12,373
Modeled Residue Count: 1,576
Deposited Residue Count: 1,612
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, B, E [auth C], F [auth D]	397	Mycolicibacterium thermoresistibile	Mutation(s): 0 Gene Names: dnaN, RMCT_1113
UniProt
Find proteins for G7CIP4 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CIP4 Go to UniProtKB: G7CIP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G7CIP4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV 1 peptide	C [auth E], D [auth F], G, H	6	Mycobacterium tuberculosis	Mutation(s): 0 EC: 2.7.7.7
UniProt
Find proteins for P9WNT3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNT3 Go to UniProtKB: P9WNT3
Entity Groups
UniProt Group	P9WNT3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain Q [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth D]	I [auth A], J [auth B], K [auth B], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain Q [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain Q [auth D]
ACE (Subject of Investigation/LOI) Query on ACE Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain R [auth G] SDF format, chain T [auth H] SDF format, chain O [auth F] MOL2 format, chain M [auth E] MOL2 format, chain R [auth G] MOL2 format, chain T [auth H] MOL2 format, chain O [auth F] mmCIF format, chain M [auth E] mmCIF format, chain R [auth G] mmCIF format, chain T [auth H] mmCIF format, chain O [auth F]	M [auth E], O [auth F], R [auth G], T [auth H]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain O [auth F] Focus chain R [auth G] Focus chain T [auth H] Interactions & Density Focus chain M [auth E] Focus chain O [auth F] Focus chain R [auth G] Focus chain T [auth H]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NH2 (Subject of Investigation/LOI) Query on NH2 Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain S [auth G] SDF format, chain U [auth H] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain S [auth G] MOL2 format, chain U [auth H] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain S [auth G] mmCIF format, chain U [auth H]	N [auth E], P [auth F], S [auth G], U [auth H]	AMINO GROUP H₂ N QGZKDVFQNNGYKY-UHFFFAOYSA-N		Interactions Focus chain N [auth E] Focus chain P [auth F] Focus chain S [auth G] Focus chain U [auth H] Interactions & Density Focus chain N [auth E] Focus chain P [auth F] Focus chain S [auth G] Focus chain U [auth H]