9UVL | pdb_00009uvl

Crystal structure of AGAP1-GDP complex

PDB DOI: https://doi.org/10.2210/pdb9UVL/pdb

Classification: CELL INVASION
Organism(s): Homo sapiens
Expression System: Escherichia phage EcSzw_1
Mutation(s): No

Deposited: 2025-05-10 Released: 2026-04-15
Deposition Author(s): Zhang, S., Zhang, Y., Cheng, N., Wang, J., Li, Z., Meng, G., Zhang, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.268 (Depositor), 0.266 (DCC)
R-Value Work:
0.219 (Depositor), 0.228 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

AGAP1 and noncanonical GDP binding regulate triple-negative breast cancer development.

Zhang, Y., Zhang, S., Deng, X., Cheng, N., Wang, J., Huang, H., Zhuo, Z., Ye, S., Yu, X., Li, Z., Meng, G., Zhang, H.

(2026) Cell Mol Life Sci 83

PubMed: 42002626 Search on PubMed
DOI: https://doi.org/10.1007/s00018-026-06196-z
Primary Citation Related Structures:
9UVL

Organizational Affiliation

Department of Geriatrics, Medical Center on Aging of Ruijin Hospital, Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, P. R. China.

Macromolecule Content

Total Structure Weight: 158.9 kDa
Atom Count: 10,716
Modeled Residue Count: 1,315
Deposited Residue Count: 1,376
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1	A, B, C, D, E A, B, C, D, E, F, G, H	172	Homo sapiens	Mutation(s): 0 Gene Names: AGAP1, CENTG2, KIAA1099
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPQ3 (Homo sapiens) Explore Q9UPQ3 Go to UniProtKB: Q9UPQ3
PHAROS: Q9UPQ3 GTEx: ENSG00000157985
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UPQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain HA [auth G] SDF format, chain EA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain HA [auth G] MOL2 format, chain EA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain HA [auth G] mmCIF format, chain EA [auth F]	EA [auth F] HA [auth G] I [auth B] J [auth B] P [auth D] EA [auth F], HA [auth G], I [auth B], J [auth B], P [auth D], Q [auth D], W [auth E], X [auth E]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain EA [auth F] Focus chain HA [auth G] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain EA [auth F] Focus chain HA [auth G] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain W [auth E] Focus chain X [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain KA [auth G] SDF format, chain K [auth B] SDF format, chain JA [auth G] SDF format, chain IA [auth G] SDF format, chain GA [auth F] SDF format, chain FA [auth F] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain KA [auth G] MOL2 format, chain K [auth B] MOL2 format, chain JA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain KA [auth G] mmCIF format, chain K [auth B] mmCIF format, chain JA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] FA [auth F] AA [auth E], BA [auth E], CA [auth E], DA [auth E], FA [auth F], GA [auth F], IA [auth G], JA [auth G], K [auth B], KA [auth G], L [auth B], M [auth B], N [auth B], O [auth B], R [auth D], S [auth D], T [auth D], U [auth D], V [auth D], Y [auth E], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain K [auth B] Focus chain KA [auth G] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain K [auth B] Focus chain KA [auth G] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Focus chain Z [auth E]