6PWZ | pdb_00006pwz

Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine

PDB DOI: https://doi.org/10.2210/pdb6PWZ/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-24 Released: 2020-07-29
Deposition Author(s): Cuthbert, B.J., Goulding, C.W.
Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.199 (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

Incorporation of novel azido-nucleotides into RNA

Nainar, S., Cuthbert, B.J., Goulding, C.W., Spitale, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 229.2 kDa
Atom Count: 13,675
Modeled Residue Count: 1,696
Deposited Residue Count: 2,000
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine-cytidine kinase 2	A, B, C, D, E A, B, C, D, E, F, G, H	250	Homo sapiens	Mutation(s): 0 Gene Names: UCK2, UMPK EC: 2.7.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZX2 (Homo sapiens) Explore Q9BZX2 Go to UniProtKB: Q9BZX2
PHAROS: Q9BZX2 GTEx: ENSG00000143179
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BZX2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6D (Subject of Investigation/LOI) Query on P6D Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain MA [auth E] SDF format, chain WA [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain WA [auth H] mmCIF format, chain FA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain WA [auth H]	FA [auth D], MA [auth E], WA [auth H]	2'-azidocytidine C₉ H₁₃ N₆ O₄ SXKUZFQHWHCRFO-XVFCMESISA-N		Interactions Focus chain FA [auth D] Focus chain MA [auth E] Focus chain WA [auth H] Interactions & Density Focus chain FA [auth D] Focus chain MA [auth E] Focus chain WA [auth H]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain I [auth A] SDF format, chain NA [auth F] SDF format, chain P [auth B] SDF format, chain RA [auth G] SDF format, chain T [auth C] SDF format, chain TA [auth H] SDF format, chain Y [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth H] MOL2 format, chain Y [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth H] mmCIF format, chain Y [auth D]	GA [auth E] I [auth A] NA [auth F] P [auth B] RA [auth G] GA [auth E], I [auth A], NA [auth F], P [auth B], RA [auth G], T [auth C], TA [auth H], Y [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth E] Focus chain I [auth A] Focus chain NA [auth F] Focus chain P [auth B] Focus chain RA [auth G] Focus chain T [auth C] Focus chain TA [auth H] Focus chain Y [auth D] Interactions & Density Focus chain GA [auth E] Focus chain I [auth A] Focus chain NA [auth F] Focus chain P [auth B] Focus chain RA [auth G] Focus chain T [auth C] Focus chain TA [auth H] Focus chain Y [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth G] SDF format, chain U [auth C] SDF format, chain UA [auth H] SDF format, chain V [auth C] SDF format, chain VA [auth H] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], HA [auth E], IA [auth E], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], N [auth A], O [auth A], OA [auth F], PA [auth F], Q [auth B], QA [auth F], R [auth B], S [auth B], SA [auth G], U [auth C], UA [auth H], V [auth C], VA [auth H], W [auth C], X [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth G] Focus chain U [auth C] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth G] Focus chain U [auth C] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]