7BMM | pdb_00007bmm

Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form

PDB DOI: https://doi.org/10.2210/pdb7BMM/pdb

Classification: TRANSFERASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-20 Released: 2021-04-07
Deposition Author(s): Silva, S.T.N., Romao, C.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.246 (Depositor), 0.242 (DCC)
R-Value Work:
0.194 (Depositor), 0.193 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form

Silva, S.T.N., Romao, C.

To be published.

Macromolecule Content

Total Structure Weight: 122.95 kDa
Atom Count: 9,183
Modeled Residue Count: 1,064
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PPK2 domain-containing protein	A, B, C, D	266	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0 Gene Names: DR_0132 EC: 2.7.4.1
UniProt
Find proteins for Q9RY20 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RY20 Go to UniProtKB: Q9RY20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RY20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth B], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B]	G [auth B], I [auth C], J [auth C], K [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C]