9DTP | pdb_00009dtp

GlfT2 from Nocardia brasiliensis

PDB DOI: https://doi.org/10.2210/pdb9DTP/pdb

Classification: TRANSFERASE
Organism(s): Nocardia brasiliensis ATCC 700358
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-01 Released: 2025-10-08
Deposition Author(s): Carter, A.W., Dodge, G.J., Kiessling, L.L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.258 (Depositor), 0.257 (DCC)
R-Value Work:
0.221 (Depositor), 0.221 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

GlfT2 from Nocardia brasiliensis

Carter, A.W., Dodge, G.J., Keys, A.M., Justen, A.M., Taylor, K.I., Imperiali, B., Kulik, H.J., Kiessling, L.L.

To be published.

Macromolecule Content

Total Structure Weight: 593.52 kDa
Atom Count: 39,330
Modeled Residue Count: 4,989
Deposited Residue Count: 5,328
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactofuranosyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	666	Nocardia brasiliensis ATCC 700358	Mutation(s): 0 Gene Names: O3I_000690
UniProt
Find proteins for K0EQQ2 (Nocardia brasiliensis (strain ATCC 700358 / HUJEG-1)) Explore K0EQQ2 Go to UniProtKB: K0EQQ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K0EQQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRT Query on TRT Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain HA [auth G] SDF format, chain J [auth A] SDF format, chain KA [auth H] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	DA [auth F] HA [auth G] J [auth A] KA [auth H] N [auth B] DA [auth F], HA [auth G], J [auth A], KA [auth H], N [auth B], R [auth C], V [auth D], Z [auth E]	FRAGMENT OF TRITON X-100 C₂₁ H₃₆ O₄ HEUDUECKTWTQQR-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain HA [auth G] Focus chain J [auth A] Focus chain KA [auth H] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain HA [auth G] Focus chain J [auth A] Focus chain KA [auth H] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain IA [auth G] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] 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 EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] 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 EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain MA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	AA [auth E] BA [auth E] EA [auth F] FA [auth F] IA [auth G] AA [auth E], BA [auth E], EA [auth F], FA [auth F], IA [auth G], K [auth A], L [auth A], LA [auth H], MA [auth H], O [auth B], P [auth B], S [auth C], T [auth C], W [auth D], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D]
MG Query on MG 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 M [auth B] SDF format, chain Q [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 M [auth B] MOL2 format, chain Q [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 M [auth B] mmCIF format, chain Q [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] M [auth B] CA [auth F], GA [auth G], I [auth A], JA [auth H], M [auth B], Q [auth C], U [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain M [auth B] Focus chain Q [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 M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.258 (Depositor), 0.257 (DCC)
R-Value Work: 0.221 (Depositor), 0.221 (DCC)
R-Value Observed: 0.222 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39DTP

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.026	α = 90
b = 205.045	β = 90
c = 295.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
JBluIce-EPICS	data collection
XDS	data reduction
XDS	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Carter, A.W.

Dodge, G.J.

Kiessling, L.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R01 AI126592-09
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1F31 GM148069