9Y12 | pdb_00009y12

Crystal Structure of N-Acetyl Transferase Domain-Containing Protein from Bacteroides fragilis

PDB DOI: https://doi.org/10.2210/pdb9Y12/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides fragilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-29 Released: 2025-09-10
Deposition Author(s): Kim, Y., Bigelow, L., Clancy, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.224 (Depositor), 0.195 (DCC)
R-Value Work:
0.189 (Depositor), 0.193 (DCC)
R-Value Observed:
0.199 (Depositor)

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 N-Acetyl Transferase Domain-Containing Protein from Bacteroides fragilis

Kim, Y., Bigelow, L., Clancy, L., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 154.62 kDa
Atom Count: 10,683
Modeled Residue Count: 1,216
Deposited Residue Count: 1,232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase (GNAT) family protein	A, B, C, D, E A, B, C, D, E, F, G, H	154	Bacteroides fragilis	Mutation(s): 0 Gene Names: CQW34_04244, F2Z25_15380, F2Z89_05330
UniProt
Find proteins for A0A149N1Y8 (Bacteroides fragilis) Explore A0A149N1Y8 Go to UniProtKB: A0A149N1Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A149N1Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain GA [auth G] SDF format, chain I [auth A] SDF format, chain JA [auth H] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	CA [auth F] GA [auth G] I [auth A] JA [auth H] N [auth B] CA [auth F], GA [auth G], I [auth A], JA [auth H], N [auth B], S [auth C], U [auth D], Y [auth E]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain N [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain N [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain Y [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain HA [auth G] SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain L [auth A] SDF format, chain LA [auth H] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	AA [auth E] BA [auth E] DA [auth F] EA [auth F] FA [auth F] AA [auth E], BA [auth E], DA [auth F], EA [auth F], FA [auth F], HA [auth G], IA [auth G], J [auth A], K [auth A], KA [auth H], L [auth A], LA [auth H], M [auth A], P [auth B], Q [auth B], R [auth B], T [auth C], V [auth D], W [auth D], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain Z [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain Z [auth E]	Z [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Z [auth E] Interactions & Density Focus chain Z [auth E]