9NJ1 | pdb_00009nj1

GlfT2 from Nocardia brasiliensis Bound to Galf Tetrasaccharide

PDB DOI: https://doi.org/10.2210/pdb9NJ1/pdb

Classification: TRANSFERASE
Organism(s): Nocardia brasiliensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-02-26 Released: 2026-03-11
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: 3.15 Å
R-Value Free:
0.278 (Depositor), 0.279 (DCC)
R-Value Work:
0.238 (Depositor), 0.238 (DCC)
R-Value Observed:
0.239 (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

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: 599.23 kDa
Atom Count: 39,638
Modeled Residue Count: 4,997
Deposited Residue Count: 5,328
Unique protein chains: 1

Macromolecules

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| 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	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K0EQQ2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactofuranose-(1-6)-beta-D-galactofuranose-(1-5)-beta-D-galactofuranose-(1-6)-beta-D-galactofuranose	I, J, K, L [auth M], M [auth N], I, J, K, L [auth M], M [auth N], N [auth O], O [auth P], P [auth L]	4		N/A	Interactions Focus chain I Focus chain J Focus chain K Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth L] Interactions & Density Focus chain I Focus chain J Focus chain K Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth L]
Glycosylation Resources
GlyTouCan: G99317XX GlyCosmos: G99317XX

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRT Query on TRT Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain GA [auth F] SDF format, chain IA [auth G] SDF format, chain LA [auth H] SDF format, chain U [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain GA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain U [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain GA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain U [auth B]	AA [auth D], GA [auth F], IA [auth G], LA [auth H], U [auth B]	FRAGMENT OF TRITON X-100 C₂₁ H₃₆ O₄ HEUDUECKTWTQQR-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain U [auth B] Interactions & Density Focus chain AA [auth D] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain U [auth B]
TON Query on TON Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain R [auth A] SDF format, chain X [auth C] MOL2 format, chain DA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain X [auth C]	DA [auth E], R [auth A], X [auth C]	2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL C₁₈ H₃₀ O₃ LBCZOTMMGHGTPH-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain R [auth A] Focus chain X [auth C] Interactions & Density Focus chain DA [auth E] Focus chain R [auth A] Focus chain X [auth C]
A1BYH (Subject of Investigation/LOI) Query on A1BYH Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain JA [auth G] SDF format, chain MA [auth H] SDF format, chain S [auth A] SDF format, chain V [auth B] SDF format, chain Y [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain JA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain S [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain JA [auth G] mmCIF format, chain MA [auth H] mmCIF format, chain S [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth C]	BA [auth D] EA [auth E] JA [auth G] MA [auth H] S [auth A] BA [auth D], EA [auth E], JA [auth G], MA [auth H], S [auth A], V [auth B], Y [auth C]	(2E)-12-phenoxydodec-2-en-1-ol C₁₈ H₂₈ O₂ FYHKQZDCHQMJGE-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain EA [auth E] Focus chain JA [auth G] Focus chain MA [auth H] Focus chain S [auth A] Focus chain V [auth B] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth E] Focus chain JA [auth G] Focus chain MA [auth H] Focus chain S [auth A] Focus chain V [auth B] Focus chain Y [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain HA [auth G] SDF format, chain KA [auth H] SDF format, chain Q [auth A] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D]	CA [auth E] FA [auth F] HA [auth G] KA [auth H] Q [auth A] CA [auth E], FA [auth F], HA [auth G], KA [auth H], Q [auth A], T [auth B], W [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain Q [auth A] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain Q [auth A] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.278 (Depositor), 0.279 (DCC)
R-Value Work: 0.238 (Depositor), 0.238 (DCC)
R-Value Observed: 0.239 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.21	α = 90
b = 203.912	β = 90
c = 292.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-11

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