8WW7 | pdb_00008ww7

Structure of AMPPNP-Form AsfvPrimPol Dodecamer

PDB DOI: https://doi.org/10.2210/pdb8WW7/pdb
NAKB: 8WW7
EM Map EMD-37883: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, African swine fever virus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-10-25 Released: 2025-04-30
Deposition Author(s): Shi, T.H., Guo, Y.Y., Yan, R.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of ADP-Form AsfvPrimPol Hexamer

Shi, T.H., Guo, Y.Y., Yan, R.H.

To be published.

Macromolecule Content

Total Structure Weight: 1,375.81 kDa
Atom Count: 88,330
Modeled Residue Count: 10,686
Deposited Residue Count: 11,720
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative primase C962R	C [auth A] D [auth B] E [auth C] F [auth D] G [auth E] C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth L], K, L [auth J], M [auth I], N [auth H]	972	African swine fever virus	Mutation(s): 0 Gene Names: C962R CDS
UniProt
Find proteins for A0A2X0TKI6 (African swine fever virus) Explore A0A2X0TKI6 Go to UniProtKB: A0A2X0TKI6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2X0TKI6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	A [auth M], O	26	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PAPAPAPA)-3')	B [auth N]	4	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain X [auth E] SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain P [auth A] SDF format, chain GA [auth H] SDF format, chain FA [auth I] SDF format, chain EA [auth J] SDF format, chain DA [auth K] SDF format, chain CA [auth L] SDF format, chain BA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain X [auth E] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain P [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain FA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain DA [auth K] MOL2 format, chain CA [auth L] MOL2 format, chain BA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain X [auth E] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain P [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain FA [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain DA [auth K] mmCIF format, chain CA [auth L] mmCIF format, chain BA [auth G]	BA [auth G] CA [auth L] DA [auth K] EA [auth J] FA [auth I] BA [auth G], CA [auth L], DA [auth K], EA [auth J], FA [auth I], GA [auth H], P [auth A], R [auth B], T [auth C], V [auth D], X [auth E], Z [auth F]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain BA [auth G] Focus chain CA [auth L] Focus chain DA [auth K] Focus chain EA [auth J] Focus chain FA [auth I] Focus chain GA [auth H] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain CA [auth L] Focus chain DA [auth K] Focus chain EA [auth J] Focus chain FA [auth I] Focus chain GA [auth H] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain U [auth C] SDF format, chain S [auth B] SDF format, chain Q [auth A] SDF format, chain AA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain U [auth C] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain U [auth C] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain AA [auth F]	AA [auth F] Q [auth A] S [auth B] U [auth C] W [auth D] AA [auth F], Q [auth A], S [auth B], U [auth C], W [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E]