9AVA | pdb_00009ava

Co-crystal structure of human TREX1 in complex with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb9AVA/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-01 Released: 2024-05-15
Deposition Author(s): Dehghani-Tafti, S., Dong, A., Li, Y., Xu, J., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.239 (Depositor), 0.247 (DCC)
R-Value Work:
0.202 (Depositor), 0.209 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Co-crystal structure of human TREX1 in complex with an inhibitor

Dehghani-Tafti, S., Dong, A., Li, Y., Xu, J., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 304.79 kDa
Atom Count: 20,087
Modeled Residue Count: 2,528
Deposited Residue Count: 2,772
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Three-prime repair exonuclease 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	231	Homo sapiens	Mutation(s): 0 Gene Names: TREX1 EC: 3.1.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NSU2 (Homo sapiens) Explore Q9NSU2 Go to UniProtKB: Q9NSU2
PHAROS: Q9NSU2 GTEx: ENSG00000213689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NSU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AG1 (Subject of Investigation/LOI) Query on A1AG1 Download:Ideal Coordinates CCD File SDF format, chain XA [auth H] SDF format, chain X [auth C] SDF format, chain SA [auth G] SDF format, chain S [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth F] SDF format, chain KB [auth L] SDF format, chain IB [auth K] SDF format, chain HA [auth E] SDF format, chain FB [auth J] SDF format, chain DA [auth D] SDF format, chain BB [auth I] MOL2 format, chain XA [auth H] MOL2 format, chain X [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain KB [auth L] MOL2 format, chain IB [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain FB [auth J] MOL2 format, chain DA [auth D] MOL2 format, chain BB [auth I] mmCIF format, chain XA [auth H] mmCIF format, chain X [auth C] mmCIF format, chain SA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain KB [auth L] mmCIF format, chain IB [auth K] mmCIF format, chain HA [auth E] mmCIF format, chain FB [auth J] mmCIF format, chain DA [auth D] mmCIF format, chain BB [auth I]	BB [auth I] DA [auth D] FB [auth J] HA [auth E] IB [auth K] BB [auth I], DA [auth D], FB [auth J], HA [auth E], IB [auth K], KB [auth L], MA [auth F], N [auth A], S [auth B], SA [auth G], X [auth C], XA [auth H]	(2R)-2-[(5R,6S,8R,9aS)-8-amino-1-oxo-5-(2-phenylethyl)hexahydro-1H-pyrrolo[1,2-a][1,4]diazepin-2(3H)-yl]-N-[(3,4-dichlorophenyl)methyl]-4-methylpentanamide C₂₉ H₃₈ Cl₂ N₄ O₂ OUNCNWBQPZONLJ-CIMSBJEKSA-N		Interactions Focus chain BB [auth I] Focus chain DA [auth D] Focus chain FB [auth J] Focus chain HA [auth E] Focus chain IB [auth K] Focus chain KB [auth L] Focus chain MA [auth F] Focus chain N [auth A] Focus chain S [auth B] Focus chain SA [auth G] Focus chain X [auth C] Focus chain XA [auth H] Interactions & Density Focus chain BB [auth I] Focus chain DA [auth D] Focus chain FB [auth J] Focus chain HA [auth E] Focus chain IB [auth K] Focus chain KB [auth L] Focus chain MA [auth F] Focus chain N [auth A] Focus chain S [auth B] Focus chain SA [auth G] Focus chain X [auth C] Focus chain XA [auth H]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain WA [auth H] SDF format, chain W [auth C] SDF format, chain RA [auth G] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth F] SDF format, chain JB [auth L] SDF format, chain HB [auth K] SDF format, chain EB [auth J] SDF format, chain CA [auth D] SDF format, chain AB [auth I] MOL2 format, chain WA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain JB [auth L] MOL2 format, chain HB [auth K] MOL2 format, chain EB [auth J] MOL2 format, chain CA [auth D] MOL2 format, chain AB [auth I] mmCIF format, chain WA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain JB [auth L] mmCIF format, chain HB [auth K] mmCIF format, chain EB [auth J] mmCIF format, chain CA [auth D] mmCIF format, chain AB [auth I]	AB [auth I] CA [auth D] EB [auth J] HB [auth K] JB [auth L] AB [auth I], CA [auth D], EB [auth J], HB [auth K], JB [auth L], LA [auth F], M [auth A], R [auth B], RA [auth G], W [auth C], WA [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain CA [auth D] Focus chain EB [auth J] Focus chain HB [auth K] Focus chain JB [auth L] Focus chain LA [auth F] Focus chain M [auth A] Focus chain R [auth B] Focus chain RA [auth G] Focus chain W [auth C] Focus chain WA [auth H] Interactions & Density Focus chain AB [auth I] Focus chain CA [auth D] Focus chain EB [auth J] Focus chain HB [auth K] Focus chain JB [auth L] Focus chain LA [auth F] Focus chain M [auth A] Focus chain R [auth B] Focus chain RA [auth G] Focus chain W [auth C] Focus chain WA [auth H]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain Z [auth C] SDF format, chain YA [auth H] SDF format, chain Y [auth C] SDF format, chain VA [auth G] SDF format, chain V [auth B] SDF format, chain UA [auth G] SDF format, chain U [auth B] SDF format, chain TA [auth G] SDF format, chain T [auth B] SDF format, chain QA [auth F] SDF format, chain Q [auth A] SDF format, chain PA [auth F] SDF format, chain P [auth A] SDF format, chain OA [auth F] SDF format, chain O [auth A] SDF format, chain NA [auth F] SDF format, chain LB [auth L] SDF format, chain KA [auth E] SDF format, chain JA [auth E] SDF format, chain IA [auth E] SDF format, chain GB [auth J] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DB [auth I] SDF format, chain CB [auth I] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain ZA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain LB [auth L] MOL2 format, chain KA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain GB [auth J] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth I] MOL2 format, chain CB [auth I] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain ZA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain LB [auth L] mmCIF format, chain KA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain GB [auth J] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth I] mmCIF format, chain CB [auth I] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CB [auth I] DB [auth I] EA [auth D] AA [auth C], BA [auth C], CB [auth I], DB [auth I], EA [auth D], FA [auth D], GA [auth D], GB [auth J], IA [auth E], JA [auth E], KA [auth E], LB [auth L], NA [auth F], O [auth A], OA [auth F], P [auth A], PA [auth F], Q [auth A], QA [auth F], T [auth B], TA [auth G], U [auth B], UA [auth G], V [auth B], VA [auth G], Y [auth C], YA [auth H], Z [auth C], ZA [auth H]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LB [auth L] Focus chain NA [auth F] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth B] Focus chain VA [auth G] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LB [auth L] Focus chain NA [auth F] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth B] Focus chain VA [auth G] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H]