6VR0 | pdb_00006vr0

Agrobacterium Tumefaciens ADP-glucose pyrophosphorylase W106A

PDB DOI: https://doi.org/10.2210/pdb6VR0/pdb

Classification: TRANSFERASE
Organism(s): Agrobacterium tumefaciens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-02-06 Released: 2021-02-17
Deposition Author(s): Mascarenhas, R.N., Liu, D., Ballicora, M., Iglesias, A., Asencion, M., Figueroa, C.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.243 (Depositor)
R-Value Work:
0.214 (Depositor)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Currently 6VR0 does not have a validation slider image.

This is version 1.1 of the entry. See complete history.

Literature

Agrobacterium Tumefaciens ADP-glucose pyrophosphorylase W106A

Mascarenhas, R.N., Liu, D., Ballicora, M., Iglesias, A., Asencion, M., Figueroa, C., Esper, M., Aleanzi, M.

To be published.

Macromolecule Content

Total Structure Weight: 470.46 kDa
Atom Count: 32,581
Modeled Residue Count: 4,040
Deposited Residue Count: 4,130
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	413	Agrobacterium tumefaciens	Mutation(s): 1 Gene Names: glgC, SY94_4053 EC: 2.7.7.27
UniProt
Find proteins for P39669 (Rhizobium radiobacter) Explore P39669 Go to UniProtKB: P39669
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39669
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
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 BC [auth I] SDF format, chain CA [auth C] SDF format, chain CB [auth F] SDF format, chain CC [auth I] SDF format, chain DC [auth I] SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain EC [auth I] SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain FC [auth I] SDF format, chain GA [auth C] SDF format, chain GB [auth G] SDF format, chain GC [auth I] SDF format, chain HB [auth G] SDF format, chain HC [auth I] 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 JC [auth I] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain KB [auth G] SDF format, chain KC [auth I] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth G] SDF format, chain LC [auth I] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MB [auth G] SDF format, chain MC [auth J] SDF format, chain N [auth A] SDF format, chain NB [auth G] SDF format, chain NC [auth J] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain OB [auth G] SDF format, chain OC [auth J] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain PB [auth G] SDF format, chain PC [auth J] SDF format, chain QA [auth E] SDF format, chain QB [auth H] SDF format, chain QC [auth J] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain RB [auth H] SDF format, chain RC [auth J] SDF format, chain SA [auth E] SDF format, chain SB [auth H] SDF format, chain SC [auth J] SDF format, chain TA [auth E] SDF format, chain TB [auth H] SDF format, chain TC [auth J] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain UB [auth H] SDF format, chain UC [auth J] SDF format, chain V [auth B] SDF format, chain VB [auth H] SDF format, chain VC [auth J] SDF format, chain WA [auth E] SDF format, chain WB [auth H] SDF format, chain XA [auth E] SDF format, chain XB [auth H] SDF format, chain Y [auth C] SDF format, chain YA [auth E] SDF format, chain YB [auth H] SDF format, chain Z [auth C] SDF format, chain ZA [auth F] SDF format, chain ZB [auth I] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain VA [auth E] SDF format, chain T [auth B] SDF format, chain S [auth A] SDF format, chain Q [auth A] SDF format, chain NA [auth D] SDF format, chain HA [auth D] SDF format, chain DB [auth F] SDF format, chain DA [auth C] SDF format, chain AC [auth I] 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 BC [auth I] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain CC [auth I] MOL2 format, chain DC [auth I] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain EC [auth I] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain FC [auth I] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain GC [auth I] MOL2 format, chain HB [auth G] MOL2 format, chain HC [auth I] 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 JC [auth I] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain KC [auth I] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth G] MOL2 format, chain LC [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth G] MOL2 format, chain MC [auth J] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth G] MOL2 format, chain NC [auth J] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain OB [auth G] MOL2 format, chain OC [auth J] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain PB [auth G] MOL2 format, chain PC [auth J] MOL2 format, chain QA [auth E] MOL2 format, chain QB [auth H] MOL2 format, chain QC [auth J] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth H] MOL2 format, chain RC [auth J] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth H] MOL2 format, chain SC [auth J] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth H] MOL2 format, chain TC [auth J] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain UB [auth H] MOL2 format, chain UC [auth J] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth H] MOL2 format, chain VC [auth J] MOL2 format, chain WA [auth E] MOL2 format, chain WB [auth H] MOL2 format, chain XA [auth E] MOL2 format, chain XB [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth E] MOL2 format, chain YB [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth F] MOL2 format, chain ZB [auth I] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain DB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain AC [auth I] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain BC [auth I] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain CC [auth I] mmCIF format, chain DC [auth I] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain EC [auth I] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain FC [auth I] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth G] mmCIF format, chain GC [auth I] mmCIF format, chain HB [auth G] mmCIF format, chain HC [auth I] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth G] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth G] mmCIF format, chain JC [auth I] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth G] mmCIF format, chain KC [auth I] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth G] mmCIF format, chain LC [auth I] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth G] mmCIF format, chain MC [auth J] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth G] mmCIF format, chain NC [auth J] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain OB [auth G] mmCIF format, chain OC [auth J] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain PB [auth G] mmCIF format, chain PC [auth J] mmCIF format, chain QA [auth E] mmCIF format, chain QB [auth H] mmCIF format, chain QC [auth J] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain RB [auth H] mmCIF format, chain RC [auth J] mmCIF format, chain SA [auth E] mmCIF format, chain SB [auth H] mmCIF format, chain SC [auth J] mmCIF format, chain TA [auth E] mmCIF format, chain TB [auth H] mmCIF format, chain TC [auth J] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain UB [auth H] mmCIF format, chain UC [auth J] mmCIF format, chain V [auth B] mmCIF format, chain VB [auth H] mmCIF format, chain VC [auth J] mmCIF format, chain WA [auth E] mmCIF format, chain WB [auth H] mmCIF format, chain XA [auth E] mmCIF format, chain XB [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth E] mmCIF format, chain YB [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth F] mmCIF format, chain ZB [auth I] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain DB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain AC [auth I]	AA [auth C] AB [auth F] AC [auth I] BA [auth C] BB [auth F] AA [auth C], AB [auth F], AC [auth I], BA [auth C], BB [auth F], BC [auth I], CA [auth C], CB [auth F], CC [auth I], DA [auth C], DB [auth F], DC [auth I], EA [auth C], EB [auth F], EC [auth I], FA [auth C], FB [auth F], FC [auth I], GA [auth C], GB [auth G], GC [auth I], HA [auth D], HB [auth G], HC [auth I], IA [auth D], IB [auth G], JA [auth D], JB [auth G], JC [auth I], K [auth A], KA [auth D], KB [auth G], KC [auth I], L [auth A], LA [auth D], LB [auth G], LC [auth I], M [auth A], MA [auth D], MB [auth G], MC [auth J], N [auth A], NA [auth D], NB [auth G], NC [auth J], O [auth A], OA [auth D], OB [auth G], OC [auth J], P [auth A], PA [auth E], PB [auth G], PC [auth J], Q [auth A], QA [auth E], QB [auth H], QC [auth J], R [auth A], RA [auth E], RB [auth H], RC [auth J], S [auth A], SA [auth E], SB [auth H], SC [auth J], T [auth B], TA [auth E], TB [auth H], TC [auth J], U [auth B], UA [auth E], UB [auth H], UC [auth J], V [auth B], VA [auth E], VB [auth H], VC [auth J], W [auth B], WA [auth E], WB [auth H], X [auth B], XA [auth E], XB [auth H], Y [auth C], YA [auth E], YB [auth H], Z [auth C], ZA [auth F], ZB [auth I]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain AC [auth I] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain BC [auth I] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain CC [auth I] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain DC [auth I] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain EC [auth I] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain FC [auth I] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain GC [auth I] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain HC [auth I] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain JC [auth I] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain KC [auth I] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain LC [auth I] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain MC [auth J] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain NC [auth J] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain OC [auth J] Focus chain P [auth A] Focus chain PA [auth E] Focus chain PB [auth G] Focus chain PC [auth J] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain QB [auth H] Focus chain QC [auth J] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain RC [auth J] Focus chain S [auth A] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain SC [auth J] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain TC [auth J] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain UC [auth J] Focus chain V [auth B] Focus chain VA [auth E] Focus chain VB [auth H] Focus chain VC [auth J] Focus chain W [auth B] Focus chain WA [auth E] Focus chain WB [auth H] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth H] Focus chain Y [auth C] Focus chain YA [auth E] Focus chain YB [auth H] Focus chain Z [auth C] Focus chain ZA [auth F] Focus chain ZB [auth I]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain IC [auth I] MOL2 format, chain IC [auth I] mmCIF format, chain IC [auth I]	IC [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IC [auth I]