8ZD3 | pdb_00008zd3

Crystal structure of ALPK1-N+K in complex with CDP-heptose

PDB DOI: https://doi.org/10.2210/pdb8ZD3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Insect expression vector pBlueBacmsGCB1His
Mutation(s): No

Deposited: 2024-05-01 Released: 2025-05-07
Deposition Author(s): She, Y., Ding, J.J., Shao, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free:
0.269 (Depositor), 0.269 (DCC)
R-Value Work:
0.240 (Depositor), 0.239 (DCC)
R-Value Observed:
0.241 (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

crystal structure of Alpha-kinase 1 N+K in complex with CDP-hep

She, Y., Ding, J., Shao, F.

To be published.

Macromolecule Content

Total Structure Weight: 169.84 kDa
Atom Count: 11,342
Modelled Residue Count: 1,378
Deposited Residue Count: 1,484
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-protein kinase 1	A, C	456	Homo sapiens	Mutation(s): 0 Gene Names: ALPK1, KIAA1527, LAK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QP1 (Homo sapiens) Explore Q96QP1 Go to UniProtKB: Q96QP1
PHAROS: Q96QP1 GTEx: ENSG00000073331
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96QP1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-protein kinase 1	B, D	286	Homo sapiens	Mutation(s): 0 Gene Names: ALPK1, KIAA1527, LAK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QP1 (Homo sapiens) Explore Q96QP1 Go to UniProtKB: Q96QP1
PHAROS: Q96QP1 GTEx: ENSG00000073331
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96QP1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDP (Subject of Investigation/LOI) Query on CDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C]	E [auth A], H [auth C]	CYTIDINE-5'-DIPHOSPHATE C₉ H₁₅ N₃ O₁₁ P₂ ZWIADYZPOWUWEW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]
A1L1P (Subject of Investigation/LOI) Query on A1L1P Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C]	F [auth A], I [auth C]	(2R,3S,4S,5S,6R)-6-[(1S)-1,2-bis(oxidanyl)ethyl]oxane-2,3,4,5-tetrol C₇ H₁₄ O₇ BGWQRWREUZVRGI-KLJZZCKASA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth D] MOL2 format, chain G [auth B] MOL2 format, chain J [auth D] mmCIF format, chain G [auth B] mmCIF format, chain J [auth D]	G [auth B], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]