9VWG | pdb_00009vwg

Structure of 16-mer V.cholerae dGTPase H114A bound to dGTP and dAMP

PDB DOI: https://doi.org/10.2210/pdb9VWG/pdb
EM Map EMD-65396: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-07-17 Released: 2026-07-22
Deposition Author(s): Shi, M., Li, P.P., Li, Q.J., Gao, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9VWG

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

Literature

Structure of Vdg octamer

Shi, M.

To be published.

Macromolecule Content

Total Structure Weight: 747.92 kDa
Atom Count: 52,432
Modeled Residue Count: 6,432
Deposited Residue Count: 6,432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyguanosinetriphosphate triphosphohydrolase-like protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	402	Vibrio cholerae	Mutation(s): 1 Gene Names: dgt, D6U24_19295, ERS013200_04025, KIN13_18180
UniProt
Find proteins for A0A0H6GV99 (Vibrio cholerae) Explore A0A0H6GV99 Go to UniProtKB: A0A0H6GV99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H6GV99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGT (Subject of Investigation/LOI) Query on DGT Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain S [auth B] SDF format, chain SA [auth O] SDF format, chain UA [auth P] SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain U [auth C] SDF format, chain QA [auth N] SDF format, chain Q [auth A] SDF format, chain OA [auth M] SDF format, chain MA [auth L] SDF format, chain KA [auth K] SDF format, chain IA [auth J] SDF format, chain GA [auth I] SDF format, chain EA [auth H] SDF format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth O] MOL2 format, chain UA [auth P] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain U [auth C] MOL2 format, chain QA [auth N] MOL2 format, chain Q [auth A] MOL2 format, chain OA [auth M] MOL2 format, chain MA [auth L] MOL2 format, chain KA [auth K] MOL2 format, chain IA [auth J] MOL2 format, chain GA [auth I] MOL2 format, chain EA [auth H] MOL2 format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth O] mmCIF format, chain UA [auth P] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain U [auth C] mmCIF format, chain QA [auth N] mmCIF format, chain Q [auth A] mmCIF format, chain OA [auth M] mmCIF format, chain MA [auth L] mmCIF format, chain KA [auth K] mmCIF format, chain IA [auth J] mmCIF format, chain GA [auth I] mmCIF format, chain EA [auth H] mmCIF format, chain AA [auth F]	AA [auth F] CA [auth G] EA [auth H] GA [auth I] IA [auth J] AA [auth F], CA [auth G], EA [auth H], GA [auth I], IA [auth J], KA [auth K], MA [auth L], OA [auth M], Q [auth A], QA [auth N], S [auth B], SA [auth O], U [auth C], UA [auth P], W [auth D], Y [auth E]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ HAAZLUGHYHWQIW-KVQBGUIXSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain Q [auth A] Focus chain QA [auth N] Focus chain S [auth B] Focus chain SA [auth O] Focus chain U [auth C] Focus chain UA [auth P] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain Q [auth A] Focus chain QA [auth N] Focus chain S [auth B] Focus chain SA [auth O] Focus chain U [auth C] Focus chain UA [auth P] Focus chain W [auth D] Focus chain Y [auth E]
D5M (Subject of Investigation/LOI) Query on D5M Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain VA [auth P] SDF format, chain V [auth C] SDF format, chain TA [auth O] SDF format, chain RA [auth N] SDF format, chain R [auth A] SDF format, chain PA [auth M] SDF format, chain NA [auth L] SDF format, chain LA [auth K] SDF format, chain JA [auth J] SDF format, chain HA [auth I] SDF format, chain FA [auth H] SDF format, chain DA [auth G] SDF format, chain BA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain VA [auth P] MOL2 format, chain V [auth C] MOL2 format, chain TA [auth O] MOL2 format, chain RA [auth N] MOL2 format, chain R [auth A] MOL2 format, chain PA [auth M] MOL2 format, chain NA [auth L] MOL2 format, chain LA [auth K] MOL2 format, chain JA [auth J] MOL2 format, chain HA [auth I] MOL2 format, chain FA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain VA [auth P] mmCIF format, chain V [auth C] mmCIF format, chain TA [auth O] mmCIF format, chain RA [auth N] mmCIF format, chain R [auth A] mmCIF format, chain PA [auth M] mmCIF format, chain NA [auth L] mmCIF format, chain LA [auth K] mmCIF format, chain JA [auth J] mmCIF format, chain HA [auth I] mmCIF format, chain FA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] DA [auth G] FA [auth H] HA [auth I] JA [auth J] BA [auth F], DA [auth G], FA [auth H], HA [auth I], JA [auth J], LA [auth K], NA [auth L], PA [auth M], R [auth A], RA [auth N], T [auth B], TA [auth O], V [auth C], VA [auth P], X [auth D], Z [auth E]	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₆ P KHWCHTKSEGGWEX-RRKCRQDMSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain R [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain TA [auth O] Focus chain V [auth C] Focus chain VA [auth P] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain R [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain TA [auth O] Focus chain V [auth C] Focus chain VA [auth P] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17.1_3660
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-07-22
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.