8AKD | pdb_00008akd

Human Sirt6 in complex with ADP-ribose and fragment 1-methyl-L-histidine

PDB DOI: https://doi.org/10.2210/pdb8AKD/pdb

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

Deposited: 2022-07-29 Released: 2023-08-16
Deposition Author(s): You, W., Steegborn, C.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.202 (Depositor), 0.211 (DCC)
R-Value Work:
0.176 (Depositor)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Development of novel Sirtuin 6 inhibitors and activators based on a protein crystallography-based fragment screen

You, W., Steegborn, C.

To be published.

Macromolecule Content

Total Structure Weight: 69.74 kDa
Atom Count: 4,658
Modeled Residue Count: 559
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-6	A, B	302	Homo sapiens	Mutation(s): 0 Gene Names: SIRT6, SIR2L6 EC: 2.3.1.286 (PDB Primary Data), 2.4.2 (UniProt), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6T7 (Homo sapiens) Explore Q8N6T7 Go to UniProtKB: Q8N6T7
PHAROS: Q8N6T7 GTEx: ENSG00000077463
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N6T7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 Query on AR6 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A], K [auth B]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-ZQSHOCFMSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
HIC (Subject of Investigation/LOI) Query on HIC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	E [auth A], M [auth B]	4-METHYL-HISTIDINE C₇ H₁₁ N₃ O₂ BRMWTNUJHUMWMS-LURJTMIESA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth A]	G [auth A] H [auth A] I [auth A] N [auth B] O [auth B] G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B]	D [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]