3S29

The crystal structure of sucrose synthase-1 from Arabidopsis thaliana and its functional implications.

PDB DOI: https://doi.org/10.2210/pdb3S29/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-05-16 Released: 2011-08-24
Deposition Author(s): Zheng, Y.I., Garavito, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.234
R-Value Work: 0.185
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 762.55 kDa
Atom Count: 51,480
Modelled Residue Count: 6,274
Deposited Residue Count: 6,528
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose synthase 1	A, B, C, D, E A, B, C, D, E, F, G, H	816	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At5g20830, SUS1, T1M15.230 EC: 2.4.1.13
UniProt
Find proteins for P49040 (Arabidopsis thaliana) Explore P49040 Go to UniProtKB: P49040
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49040
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain FB [auth G] SDF format, chain I [auth A] SDF format, chain OA [auth E] SDF format, chain OB [auth H] SDF format, chain R [auth B] SDF format, chain WA [auth F] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain OB [auth H] MOL2 format, chain R [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain Y [auth C]	FA [auth D] FB [auth G] I [auth A] OA [auth E] OB [auth H] FA [auth D], FB [auth G], I [auth A], OA [auth E], OB [auth H], R [auth B], WA [auth F], Y [auth C]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain FA [auth D] Focus chain FB [auth G] Focus chain I [auth A] Focus chain OA [auth E] Focus chain OB [auth H] Focus chain R [auth B] Focus chain WA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain FB [auth G] Focus chain I [auth A] Focus chain OA [auth E] Focus chain OB [auth H] Focus chain R [auth B] Focus chain WA [auth F] Focus chain Y [auth C]
FRU Query on FRU Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain GB [auth G] SDF format, chain J [auth A] SDF format, chain PA [auth E] SDF format, chain PB [auth H] SDF format, chain S [auth B] SDF format, chain XA [auth F] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth G] MOL2 format, chain J [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain PB [auth H] MOL2 format, chain S [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain Z [auth C]	GA [auth D] GB [auth G] J [auth A] PA [auth E] PB [auth H] GA [auth D], GB [auth G], J [auth A], PA [auth E], PB [auth H], S [auth B], XA [auth F], Z [auth C]	beta-D-fructofuranose C₆ H₁₂ O₆ RFSUNEUAIZKAJO-ARQDHWQXSA-N		Interactions Focus chain GA [auth D] Focus chain GB [auth G] Focus chain J [auth A] Focus chain PA [auth E] Focus chain PB [auth H] Focus chain S [auth B] Focus chain XA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain GB [auth G] Focus chain J [auth A] Focus chain PA [auth E] Focus chain PB [auth H] Focus chain S [auth B] Focus chain XA [auth F] Focus chain Z [auth C]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain LA [auth D] SDF format, chain LB [auth G] SDF format, chain MB [auth G] SDF format, chain P [auth A] SDF format, chain TB [auth H] SDF format, chain UB [auth H] SDF format, chain W [auth B] SDF format, chain MA [auth D] SDF format, chain UA [auth E] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth G] MOL2 format, chain MB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain TB [auth H] MOL2 format, chain UB [auth H] MOL2 format, chain W [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain UA [auth E]	CB [auth F] DA [auth C] DB [auth F] LA [auth D] LB [auth G] CB [auth F], DA [auth C], DB [auth F], LA [auth D], LB [auth G], MA [auth D], MB [auth G], P [auth A], TB [auth H], UA [auth E], UB [auth H], W [auth B]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain P [auth A] Focus chain TB [auth H] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain W [auth B] Interactions & Density Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain P [auth A] Focus chain TB [auth H] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain W [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain BB [auth F] SDF format, chain HA [auth D] SDF format, chain HB [auth G] SDF format, chain IA [auth D] SDF format, chain IB [auth G] SDF format, chain JA [auth D] SDF format, chain JB [auth G] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain KB [auth G] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain QA [auth E] SDF format, chain QB [auth H] SDF format, chain RA [auth E] SDF format, chain RB [auth H] SDF format, chain SA [auth E] SDF format, chain SB [auth H] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] SDF format, chain CA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth G] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth G] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain QB [auth H] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth H] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth H] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F] MOL2 format, chain CA [auth C]	AA [auth C] AB [auth F] BA [auth C] BB [auth F] CA [auth C] AA [auth C], AB [auth F], BA [auth C], BB [auth F], CA [auth C], HA [auth D], HB [auth G], IA [auth D], IB [auth G], JA [auth D], JB [auth G], K [auth A], KA [auth D], KB [auth G], L [auth A], M [auth A], N [auth A], O [auth A], QA [auth E], QB [auth H], RA [auth E], RB [auth H], SA [auth E], SB [auth H], T [auth B], TA [auth E], U [auth B], V [auth B], YA [auth F], ZA [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain QA [auth E] Focus chain QB [auth H] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain QA [auth E] Focus chain QB [auth H] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth F] Focus chain ZA [auth F]
K Query on K Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain NA [auth D] SDF format, chain Q [auth A] SDF format, chain VA [auth E] SDF format, chain VB [auth H] SDF format, chain X [auth B] SDF format, chain NB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain VA [auth E] MOL2 format, chain VB [auth H] MOL2 format, chain X [auth B] MOL2 format, chain NB [auth G]	EA [auth C] EB [auth F] NA [auth D] NB [auth G] Q [auth A] EA [auth C], EB [auth F], NA [auth D], NB [auth G], Q [auth A], VA [auth E], VB [auth H], X [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain EB [auth F] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain Q [auth A] Focus chain VA [auth E] Focus chain VB [auth H] Focus chain X [auth B] Interactions & Density Focus chain EA [auth C] Focus chain EB [auth F] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain Q [auth A] Focus chain VA [auth E] Focus chain VB [auth H] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.234
R-Value Work: 0.185
R-Value Observed: 0.187
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 277.16	α = 90
b = 261.5	β = 109.27
c = 161.1	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Zheng, Y.I.

Garavito, R.M.

Revision History (Full details and data files)

Version 1.0: 2011-08-24
Type: Initial release
Version 1.1: 2011-09-14
Changes: Other
Version 1.2: 2011-10-26
Changes: Database references
Version 1.3: 2015-04-29
Changes: Non-polymer description
Version 1.4: 2018-01-24
Changes: Structure summary
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.6: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary