5L6V

Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a negative allosteric regulator adenosine monophosphate (AMP) - AGPase*AMP

PDB DOI: https://doi.org/10.2210/pdb5L6V/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: 2.67 Å
R-Value Free: 0.263
R-Value Work: 0.239
R-Value Observed: 0.240

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: 788.53 kDa
Atom Count: 53,530
Modelled Residue Count: 6,646
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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	Q, R, S, T, U Q, R, S, T, U, V, W, X	2		N/A	Interactions Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth H] SDF format, chain HA [auth I] SDF format, chain IA [auth J] SDF format, chain JA [auth K] SDF format, chain KA [auth L] SDF format, chain LA [auth M] SDF format, chain MA [auth N] SDF format, chain NA [auth O] SDF format, chain OA [auth P] SDF format, chain Y [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain JA [auth K] MOL2 format, chain KA [auth L] MOL2 format, chain LA [auth M] MOL2 format, chain MA [auth N] MOL2 format, chain NA [auth O] MOL2 format, chain OA [auth P] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B]	AA [auth C] BA [auth D] DA [auth E] EA [auth F] FA [auth G] AA [auth C], BA [auth D], DA [auth E], EA [auth F], FA [auth G], GA [auth H], HA [auth I], IA [auth J], JA [auth K], KA [auth L], LA [auth M], MA [auth N], NA [auth O], OA [auth P], Y [auth A], Z [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain LA [auth M] Focus chain MA [auth N] Focus chain NA [auth O] Focus chain OA [auth P] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain LA [auth M] Focus chain MA [auth N] Focus chain NA [auth O] Focus chain OA [auth P] Focus chain Y [auth A] Focus chain Z [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] MOL2 format, chain CA [auth D]	CA [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth D] Interactions & Density Focus chain CA [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	Q, R, S, T, U Q, R, S, T, U, V, W, X	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.263
R-Value Work: 0.239
R-Value Observed: 0.240
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.883	α = 90
b = 148.193	β = 115.48
c = 180.164	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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary