5L6S

Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a positive allosteric regulator beta-fructose-1,6-diphosphate (FBP) - AGPase*FBP

PDB DOI: https://doi.org/10.2210/pdb5L6S/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-31 Released: 2016-09-07
Deposition Author(s): Cifuente, J.O., Albesa-Jove, D., Comino, N., Madariaga-Marcos, J., Agirre, J., Lopez-Fernandez, S., Garcia-Alija, M., Guerin, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.272
R-Value Work: 0.234
R-Value Observed: 0.235

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 785.24 kDa
Atom Count: 45,056
Modelled Residue Count: 6,214
Deposited Residue Count: 6,896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate adenylyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	431	Escherichia coli K-12	Mutation(s): 0 Gene Names: glgC, b3430, JW3393 EC: 2.7.7.27
UniProt
Find proteins for P0A6V1 (Escherichia coli (strain K12)) Explore P0A6V1 Go to UniProtKB: P0A6V1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6V1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain EB [auth L] SDF format, chain MA [auth G] SDF format, chain UA [auth I] SDF format, chain Z [auth C] MOL2 format, chain EB [auth L] MOL2 format, chain MA [auth G] MOL2 format, chain UA [auth I] MOL2 format, chain Z [auth C]	EB [auth L], MA [auth G], UA [auth I], Z [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain EB [auth L] Focus chain MA [auth G] Focus chain UA [auth I] Focus chain Z [auth C] Interactions & Density Focus chain EB [auth L] Focus chain MA [auth G] Focus chain UA [auth I] Focus chain Z [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth K] SDF format, chain BA [auth D] SDF format, chain BB [auth L] SDF format, chain CA [auth D] SDF format, chain CB [auth L] SDF format, chain DA [auth D] SDF format, chain DB [auth L] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain FB [auth P] SDF format, chain GA [auth E] SDF format, chain GB [auth P] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain NA [auth H] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain Q [auth A] SDF format, chain QA [auth H] SDF format, chain R [auth A] SDF format, chain RA [auth I] SDF format, chain S [auth A] SDF format, chain SA [auth I] SDF format, chain T [auth B] SDF format, chain TA [auth I] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth J] SDF format, chain W [auth C] SDF format, chain WA [auth J] SDF format, chain X [auth C] SDF format, chain XA [auth J] SDF format, chain Y [auth C] SDF format, chain YA [auth K] SDF format, chain ZA [auth K] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth K] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth L] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth L] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth L] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth P] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth P] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain NA [auth H] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth I] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth I] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth J] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth J] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth K] MOL2 format, chain ZA [auth K]	AA [auth D] AB [auth K] BA [auth D] BB [auth L] CA [auth D] AA [auth D], AB [auth K], BA [auth D], BB [auth L], CA [auth D], CB [auth L], DA [auth D], DB [auth L], EA [auth E], FA [auth E], FB [auth P], GA [auth E], GB [auth P], HA [auth F], IA [auth F], JA [auth G], KA [auth G], LA [auth G], NA [auth H], OA [auth H], PA [auth H], Q [auth A], QA [auth H], R [auth A], RA [auth I], S [auth A], SA [auth I], T [auth B], TA [auth I], U [auth B], V [auth B], VA [auth J], W [auth C], WA [auth J], X [auth C], XA [auth J], Y [auth C], YA [auth K], ZA [auth K]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain AB [auth K] Focus chain BA [auth D] Focus chain BB [auth L] Focus chain CA [auth D] Focus chain CB [auth L] Focus chain DA [auth D] Focus chain DB [auth L] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain FB [auth P] Focus chain GA [auth E] Focus chain GB [auth P] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain R [auth A] Focus chain RA [auth I] Focus chain S [auth A] Focus chain SA [auth I] Focus chain T [auth B] Focus chain TA [auth I] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth J] Focus chain W [auth C] Focus chain WA [auth J] Focus chain X [auth C] Focus chain XA [auth J] Focus chain Y [auth C] Focus chain YA [auth K] Focus chain ZA [auth K] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth K] Focus chain BA [auth D] Focus chain BB [auth L] Focus chain CA [auth D] Focus chain CB [auth L] Focus chain DA [auth D] Focus chain DB [auth L] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain FB [auth P] Focus chain GA [auth E] Focus chain GB [auth P] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain R [auth A] Focus chain RA [auth I] Focus chain S [auth A] Focus chain SA [auth I] Focus chain T [auth B] Focus chain TA [auth I] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth J] Focus chain W [auth C] Focus chain WA [auth J] Focus chain X [auth C] Focus chain XA [auth J] Focus chain Y [auth C] Focus chain YA [auth K] Focus chain ZA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.272
R-Value Work: 0.234
R-Value Observed: 0.235
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.16	α = 90
b = 148.9	β = 113.1
c = 177.49	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2016-09-14
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary