5OA2

Crystal structure of ScGas2 in complex with compound 8

PDB DOI: https://doi.org/10.2210/pdb5OA2/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2017-06-20 Released: 2018-05-02
Deposition Author(s): Delso, I., Valero-Gonzalez, J., Gomollon-Bel, F., Castro-Lopez, J., Fang, W., Navratilova, I., Van Aalten, D., Tejero, T., Merino, P., Hurtado-Guerrero, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.248
R-Value Work: 0.211
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 191.31 kDa
Atom Count: 11,166
Modelled Residue Count: 1,303
Deposited Residue Count: 1,665
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,3-beta-glucanosyltransferase GAS2	A, B, C	555	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: GAS2, YLR343W, L8300.5 EC: 2.4.1
UniProt
Find proteins for Q06135 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06135 Go to UniProtKB: Q06135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06135
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	D	3		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G00024MO GlyCosmos: G00024MO GlyGen: G00024MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9PW Query on 9PW Download Ideal Coordinates CCD File SDF format, chain IA [auth C] MOL2 format, chain IA [auth C]	IA [auth C]	[4-[[1-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]-1,2,3-triazol-4-yl]methoxymethyl]phenyl]-oxidanyl-oxidanylidene-azanium C₂₈ H₄₁ N₄ O₁₈ ZVBWPZDXYFMQRY-ZJLPYKFYSA-N		Interactions Focus chain IA [auth C] Interactions & Density Focus chain IA [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A]	GA [auth B], HA [auth B], O [auth A], P [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain O [auth A] Focus chain P [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain Q [auth B] SDF format, chain QA [auth C] SDF format, chain R [auth B] SDF format, chain RA [auth C] SDF format, chain S [auth B] SDF format, chain SA [auth C] SDF format, chain T [auth B] SDF format, chain TA [auth C] SDF format, chain U [auth B] SDF format, chain UA [auth C] SDF format, chain V [auth B] SDF format, chain VA [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], OA [auth C], PA [auth C], Q [auth B], QA [auth C], R [auth B], RA [auth C], S [auth B], SA [auth C], T [auth B], TA [auth C], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
9PW	Binding MOAD: 5OA2	Kd: 9800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.248
R-Value Work: 0.211
R-Value Observed: 0.212
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.569	α = 90
b = 139.44	β = 90
c = 161.654	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary