8OJE | pdb_00008oje

Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 in complex with L-malate

PDB DOI: https://doi.org/10.2210/pdb8OJE/pdb

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

Deposited: 2023-03-24 Released: 2023-05-31
Deposition Author(s): Haesaerts, S., Loris, R., Larsen, P.B.
Funding Organization(s): United States Department of Agriculture (USDA), Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free:
0.240 (Depositor), 0.250 (DCC)
R-Value Work:
0.202 (Depositor), 0.210 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Amino acid changes that deregulate PHOSPHOENOLPYRUVATE CARBOXYLASE in plants

Meyer, T.J., Sheng, J., Haesaerts, S., Frausto, K., O'Leary, S., Loris, R., Larsen, P.B.

To be published.

Macromolecule Content

Total Structure Weight: 897.32 kDa
Atom Count: 59,093
Modeled Residue Count: 7,461
Deposited Residue Count: 7,792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxylase 1	A, B, C, D, E A, B, C, D, E, F, G, H	974	Arabidopsis thaliana	Mutation(s): 0 Gene Names: PPC1, p107, At1g53310, F12M16.21 EC: 4.1.1.31
UniProt
Find proteins for Q9MAH0 (Arabidopsis thaliana) Explore Q9MAH0 Go to UniProtKB: Q9MAH0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9MAH0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMR (Subject of Investigation/LOI) Query on LMR Download Ideal Coordinates CCD File SDF format, chain VB [auth H] SDF format, chain UA [auth E] SDF format, chain S [auth B] SDF format, chain LB [auth G] SDF format, chain LA [auth D] SDF format, chain I [auth A] SDF format, chain EB [auth F] SDF format, chain AA [auth C] MOL2 format, chain VB [auth H] MOL2 format, chain UA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain LB [auth G] MOL2 format, chain LA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain EB [auth F] MOL2 format, chain AA [auth C] mmCIF format, chain VB [auth H] mmCIF format, chain UA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain LB [auth G] mmCIF format, chain LA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain EB [auth F] mmCIF format, chain AA [auth C]	AA [auth C] EB [auth F] I [auth A] LA [auth D] LB [auth G] AA [auth C], EB [auth F], I [auth A], LA [auth D], LB [auth G], S [auth B], UA [auth E], VB [auth H]	(2S)-2-hydroxybutanedioic acid C₄ H₆ O₅ BJEPYKJPYRNKOW-REOHCLBHSA-N		Interactions Focus chain AA [auth C] Focus chain EB [auth F] Focus chain I [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain S [auth B] Focus chain UA [auth E] Focus chain VB [auth H] Interactions & Density Focus chain AA [auth C] Focus chain EB [auth F] Focus chain I [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain S [auth B] Focus chain UA [auth E] Focus chain VB [auth H]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain ZA [auth E] SDF format, chain YB [auth H] SDF format, chain YA [auth E] SDF format, chain XB [auth H] SDF format, chain XA [auth E] SDF format, chain WB [auth H] SDF format, chain WA [auth E] SDF format, chain VA [auth E] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain SB [auth G] SDF format, chain RB [auth G] SDF format, chain QB [auth G] SDF format, chain PB [auth G] SDF format, chain PA [auth D] SDF format, chain P [auth A] SDF format, chain OB [auth G] SDF format, chain OA [auth D] SDF format, chain O [auth A] SDF format, chain NB [auth G] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MB [auth G] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IB [auth F] SDF format, chain HB [auth F] SDF format, chain GB [auth F] SDF format, chain GA [auth C] SDF format, chain FB [auth F] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AB [auth E] MOL2 format, chain ZA [auth E] MOL2 format, chain YB [auth H] MOL2 format, chain YA [auth E] MOL2 format, chain XB [auth H] MOL2 format, chain XA [auth E] MOL2 format, chain WB [auth H] MOL2 format, chain WA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SB [auth G] MOL2 format, chain RB [auth G] MOL2 format, chain QB [auth G] MOL2 format, chain PB [auth G] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth G] MOL2 format, chain OA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth G] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth G] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth E] mmCIF format, chain ZA [auth E] mmCIF format, chain YB [auth H] mmCIF format, chain YA [auth E] mmCIF format, chain XB [auth H] mmCIF format, chain XA [auth E] mmCIF format, chain WB [auth H] mmCIF format, chain WA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SB [auth G] mmCIF format, chain RB [auth G] mmCIF format, chain QB [auth G] mmCIF format, chain PB [auth G] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth G] mmCIF format, chain OA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth G] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth G] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth F] mmCIF format, chain HB [auth F] mmCIF format, chain GB [auth F] mmCIF format, chain GA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth E]	AB [auth E] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AB [auth E], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], FB [auth F], GA [auth C], GB [auth F], HB [auth F], IB [auth F], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth D], MB [auth G], N [auth A], NA [auth D], NB [auth G], O [auth A], OA [auth D], OB [auth G], P [auth A], PA [auth D], PB [auth G], QB [auth G], RB [auth G], SB [auth G], T [auth B], U [auth B], V [auth B], VA [auth E], WA [auth E], WB [auth H], XA [auth E], XB [auth H], YA [auth E], YB [auth H], ZA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain QB [auth G] Focus chain RB [auth G] Focus chain SB [auth G] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain WB [auth H] Focus chain XA [auth E] Focus chain XB [auth H] Focus chain YA [auth E] Focus chain YB [auth H] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain QB [auth G] Focus chain RB [auth G] Focus chain SB [auth G] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain WB [auth H] Focus chain XA [auth E] Focus chain XB [auth H] Focus chain YA [auth E] Focus chain YB [auth H] Focus chain ZA [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain ZB [auth H] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain UB [auth G] SDF format, chain TB [auth G] SDF format, chain TA [auth D] SDF format, chain SA [auth D] SDF format, chain RA [auth D] SDF format, chain R [auth A] SDF format, chain QA [auth D] SDF format, chain Q [auth A] SDF format, chain KB [auth F] SDF format, chain KA [auth C] SDF format, chain JB [auth F] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain DB [auth E] SDF format, chain CB [auth E] SDF format, chain BB [auth E] SDF format, chain AC [auth H] MOL2 format, chain ZB [auth H] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain UB [auth G] MOL2 format, chain TB [auth G] MOL2 format, chain TA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain KA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain DB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain AC [auth H] mmCIF format, chain ZB [auth H] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain UB [auth G] mmCIF format, chain TB [auth G] mmCIF format, chain TA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain KB [auth F] mmCIF format, chain KA [auth C] mmCIF format, chain JB [auth F] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain DB [auth E] mmCIF format, chain CB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain AC [auth H]	AC [auth H] BB [auth E] CB [auth E] DB [auth E] HA [auth C] AC [auth H], BB [auth E], CB [auth E], DB [auth E], HA [auth C], IA [auth C], JA [auth C], JB [auth F], KA [auth C], KB [auth F], Q [auth A], QA [auth D], R [auth A], RA [auth D], SA [auth D], TA [auth D], TB [auth G], UB [auth G], W [auth B], X [auth B], Y [auth B], Z [auth B], ZB [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AC [auth H] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth H] Interactions & Density Focus chain AC [auth H] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth H]