3HQP

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate

PDB DOI: https://doi.org/10.2210/pdb3HQP/pdb

Classification: TRANSFERASE
Organism(s): Leishmania mexicana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-08 Released: 2010-02-16
Deposition Author(s): Morgan, H.P., Walkinshaw, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.252
R-Value Work: 0.198
R-Value Observed: 0.201

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: 888.39 kDa
Atom Count: 65,997
Modelled Residue Count: 7,968
Deposited Residue Count: 7,984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	499	Leishmania mexicana	Mutation(s): 0 Gene Names: PYK EC: 2.7.1.40
UniProt
Find proteins for Q27686 (Leishmania mexicana) Explore Q27686 Go to UniProtKB: Q27686
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q27686
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain BC [auth I] SDF format, chain GD [auth M] SDF format, chain JA [auth C] SDF format, chain QA [auth D] SDF format, chain SC [auth K] SDF format, chain XA [auth E] SDF format, chain YD [auth P] SDF format, chain ZC [auth L] SDF format, chain CA [auth B] SDF format, chain FB [auth F] SDF format, chain KC [auth J] SDF format, chain MB [auth G] SDF format, chain ND [auth N] SDF format, chain UB [auth H] SDF format, chain V [auth A] MOL2 format, chain BC [auth I] MOL2 format, chain GD [auth M] MOL2 format, chain JA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain SC [auth K] MOL2 format, chain XA [auth E] MOL2 format, chain YD [auth P] MOL2 format, chain ZC [auth L] MOL2 format, chain CA [auth B] MOL2 format, chain FB [auth F] MOL2 format, chain KC [auth J] MOL2 format, chain MB [auth G] MOL2 format, chain ND [auth N] MOL2 format, chain UB [auth H] MOL2 format, chain V [auth A]	BC [auth I] CA [auth B] FB [auth F] GD [auth M] JA [auth C] BC [auth I], CA [auth B], FB [auth F], GD [auth M], JA [auth C], KC [auth J], MB [auth G], ND [auth N], QA [auth D], SC [auth K], UB [auth H], V [auth A], XA [auth E], YD [auth P], ZC [auth L]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BC [auth I] Focus chain CA [auth B] Focus chain FB [auth F] Focus chain GD [auth M] Focus chain JA [auth C] Focus chain KC [auth J] Focus chain MB [auth G] Focus chain ND [auth N] Focus chain QA [auth D] Focus chain SC [auth K] Focus chain UB [auth H] Focus chain V [auth A] Focus chain XA [auth E] Focus chain YD [auth P] Focus chain ZC [auth L] Interactions & Density Focus chain BC [auth I] Focus chain CA [auth B] Focus chain FB [auth F] Focus chain GD [auth M] Focus chain JA [auth C] Focus chain KC [auth J] Focus chain MB [auth G] Focus chain ND [auth N] Focus chain QA [auth D] Focus chain SC [auth K] Focus chain UB [auth H] Focus chain V [auth A] Focus chain XA [auth E] Focus chain YD [auth P] Focus chain ZC [auth L]
FDP Query on FDP Download Ideal Coordinates CCD File SDF format, chain AC [auth I] SDF format, chain BA [auth B] SDF format, chain FD [auth M] SDF format, chain LB [auth G] SDF format, chain MD [auth N] SDF format, chain PA [auth D] SDF format, chain RC [auth K] SDF format, chain TB [auth H] SDF format, chain WA [auth E] SDF format, chain XD [auth P] SDF format, chain YC [auth L] SDF format, chain EB [auth F] SDF format, chain IA [auth C] SDF format, chain JC [auth J] SDF format, chain PD [auth O] SDF format, chain U [auth A] MOL2 format, chain AC [auth I] MOL2 format, chain BA [auth B] MOL2 format, chain FD [auth M] MOL2 format, chain LB [auth G] MOL2 format, chain MD [auth N] MOL2 format, chain PA [auth D] MOL2 format, chain RC [auth K] MOL2 format, chain TB [auth H] MOL2 format, chain WA [auth E] MOL2 format, chain XD [auth P] MOL2 format, chain YC [auth L] MOL2 format, chain EB [auth F] MOL2 format, chain IA [auth C] MOL2 format, chain JC [auth J] MOL2 format, chain PD [auth O] MOL2 format, chain U [auth A]	AC [auth I] BA [auth B] EB [auth F] FD [auth M] IA [auth C] AC [auth I], BA [auth B], EB [auth F], FD [auth M], IA [auth C], JC [auth J], LB [auth G], MD [auth N], PA [auth D], PD [auth O], RC [auth K], TB [auth H], U [auth A], WA [auth E], XD [auth P], YC [auth L]	2,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ YXWOAJXNVLXPMU-ZXXMMSQZSA-N		Interactions Focus chain AC [auth I] Focus chain BA [auth B] Focus chain EB [auth F] Focus chain FD [auth M] Focus chain IA [auth C] Focus chain JC [auth J] Focus chain LB [auth G] Focus chain MD [auth N] Focus chain PA [auth D] Focus chain PD [auth O] Focus chain RC [auth K] Focus chain TB [auth H] Focus chain U [auth A] Focus chain WA [auth E] Focus chain XD [auth P] Focus chain YC [auth L] Interactions & Density Focus chain AC [auth I] Focus chain BA [auth B] Focus chain EB [auth F] Focus chain FD [auth M] Focus chain IA [auth C] Focus chain JC [auth J] Focus chain LB [auth G] Focus chain MD [auth N] Focus chain PA [auth D] Focus chain PD [auth O] Focus chain RC [auth K] Focus chain TB [auth H] Focus chain U [auth A] Focus chain WA [auth E] Focus chain XD [auth P] Focus chain YC [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CC [auth I] SDF format, chain LC [auth J] SDF format, chain QD [auth O] SDF format, chain DC [auth I] SDF format, chain NB [auth G] SDF format, chain YA [auth E] MOL2 format, chain CC [auth I] MOL2 format, chain LC [auth J] MOL2 format, chain QD [auth O] MOL2 format, chain DC [auth I] MOL2 format, chain NB [auth G] MOL2 format, chain YA [auth E]	CC [auth I] DC [auth I] LC [auth J] NB [auth G] QD [auth O] CC [auth I], DC [auth I], LC [auth J], NB [auth G], QD [auth O], YA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CC [auth I] Focus chain DC [auth I] Focus chain LC [auth J] Focus chain NB [auth G] Focus chain QD [auth O] Focus chain YA [auth E] Interactions & Density Focus chain CC [auth I] Focus chain DC [auth I] Focus chain LC [auth J] Focus chain NB [auth G] Focus chain QD [auth O] Focus chain YA [auth E]
OXL Query on OXL Download Ideal Coordinates CCD File SDF format, chain DB [auth F] SDF format, chain IC [auth J] SDF format, chain LD [auth N] SDF format, chain OA [auth D] SDF format, chain SB [auth H] SDF format, chain T [auth A] SDF format, chain VA [auth E] SDF format, chain XC [auth L] SDF format, chain ZB [auth I] SDF format, chain AA [auth B] SDF format, chain ED [auth M] SDF format, chain HA [auth C] SDF format, chain KB [auth G] SDF format, chain QC [auth K] SDF format, chain WD [auth P] MOL2 format, chain DB [auth F] MOL2 format, chain IC [auth J] MOL2 format, chain LD [auth N] MOL2 format, chain OA [auth D] MOL2 format, chain SB [auth H] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth E] MOL2 format, chain XC [auth L] MOL2 format, chain ZB [auth I] MOL2 format, chain AA [auth B] MOL2 format, chain ED [auth M] MOL2 format, chain HA [auth C] MOL2 format, chain KB [auth G] MOL2 format, chain QC [auth K] MOL2 format, chain WD [auth P]	AA [auth B] DB [auth F] ED [auth M] HA [auth C] IC [auth J] AA [auth B], DB [auth F], ED [auth M], HA [auth C], IC [auth J], KB [auth G], LD [auth N], OA [auth D], QC [auth K], SB [auth H], T [auth A], VA [auth E], WD [auth P], XC [auth L], ZB [auth I]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain DB [auth F] Focus chain ED [auth M] Focus chain HA [auth C] Focus chain IC [auth J] Focus chain KB [auth G] Focus chain LD [auth N] Focus chain OA [auth D] Focus chain QC [auth K] Focus chain SB [auth H] Focus chain T [auth A] Focus chain VA [auth E] Focus chain WD [auth P] Focus chain XC [auth L] Focus chain ZB [auth I] Interactions & Density Focus chain AA [auth B] Focus chain DB [auth F] Focus chain ED [auth M] Focus chain HA [auth C] Focus chain IC [auth J] Focus chain KB [auth G] Focus chain LD [auth N] Focus chain OA [auth D] Focus chain QC [auth K] Focus chain SB [auth H] Focus chain T [auth A] Focus chain VA [auth E] Focus chain WD [auth P] Focus chain XC [auth L] Focus chain ZB [auth I]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AD [auth L] SDF format, chain CB [auth F] SDF format, chain DA [auth B] SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain JB [auth G] SDF format, chain KA [auth C] SDF format, chain KD [auth N] SDF format, chain OB [auth G] SDF format, chain OD [auth N] SDF format, chain RB [auth H] SDF format, chain S [auth A] SDF format, chain VB [auth H] SDF format, chain VD [auth P] SDF format, chain W [auth A] SDF format, chain YB [auth I] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] SDF format, chain ZD [auth P] SDF format, chain DD [auth M] SDF format, chain EC [auth I] SDF format, chain HC [auth J] SDF format, chain HD [auth M] SDF format, chain MC [auth J] SDF format, chain NA [auth D] SDF format, chain PC [auth K] SDF format, chain RA [auth D] SDF format, chain RD [auth O] SDF format, chain SD [auth O] SDF format, chain TC [auth K] SDF format, chain UA [auth E] SDF format, chain WC [auth L] MOL2 format, chain AD [auth L] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain JB [auth G] MOL2 format, chain KA [auth C] MOL2 format, chain KD [auth N] MOL2 format, chain OB [auth G] MOL2 format, chain OD [auth N] MOL2 format, chain RB [auth H] MOL2 format, chain S [auth A] MOL2 format, chain VB [auth H] MOL2 format, chain VD [auth P] MOL2 format, chain W [auth A] MOL2 format, chain YB [auth I] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain ZD [auth P] MOL2 format, chain DD [auth M] MOL2 format, chain EC [auth I] MOL2 format, chain HC [auth J] MOL2 format, chain HD [auth M] MOL2 format, chain MC [auth J] MOL2 format, chain NA [auth D] MOL2 format, chain PC [auth K] MOL2 format, chain RA [auth D] MOL2 format, chain RD [auth O] MOL2 format, chain SD [auth O] MOL2 format, chain TC [auth K] MOL2 format, chain UA [auth E] MOL2 format, chain WC [auth L]	AD [auth L] CB [auth F] DA [auth B] DD [auth M] EC [auth I] AD [auth L], CB [auth F], DA [auth B], DD [auth M], EC [auth I], GA [auth C], GB [auth F], HC [auth J], HD [auth M], JB [auth G], KA [auth C], KD [auth N], MC [auth J], NA [auth D], OB [auth G], OD [auth N], PC [auth K], RA [auth D], RB [auth H], RD [auth O], S [auth A], SD [auth O], TC [auth K], UA [auth E], VB [auth H], VD [auth P], W [auth A], WC [auth L], YB [auth I], Z [auth B], ZA [auth E], ZD [auth P]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AD [auth L] Focus chain CB [auth F] Focus chain DA [auth B] Focus chain DD [auth M] Focus chain EC [auth I] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HC [auth J] Focus chain HD [auth M] Focus chain JB [auth G] Focus chain KA [auth C] Focus chain KD [auth N] Focus chain MC [auth J] Focus chain NA [auth D] Focus chain OB [auth G] Focus chain OD [auth N] Focus chain PC [auth K] Focus chain RA [auth D] Focus chain RB [auth H] Focus chain RD [auth O] Focus chain S [auth A] Focus chain SD [auth O] Focus chain TC [auth K] Focus chain UA [auth E] Focus chain VB [auth H] Focus chain VD [auth P] Focus chain W [auth A] Focus chain WC [auth L] Focus chain YB [auth I] Focus chain Z [auth B] Focus chain ZA [auth E] Focus chain ZD [auth P] Interactions & Density Focus chain AD [auth L] Focus chain CB [auth F] Focus chain DA [auth B] Focus chain DD [auth M] Focus chain EC [auth I] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HC [auth J] Focus chain HD [auth M] Focus chain JB [auth G] Focus chain KA [auth C] Focus chain KD [auth N] Focus chain MC [auth J] Focus chain NA [auth D] Focus chain OB [auth G] Focus chain OD [auth N] Focus chain PC [auth K] Focus chain RA [auth D] Focus chain RB [auth H] Focus chain RD [auth O] Focus chain S [auth A] Focus chain SD [auth O] Focus chain TC [auth K] Focus chain UA [auth E] Focus chain VB [auth H] Focus chain VD [auth P] Focus chain W [auth A] Focus chain WC [auth L] Focus chain YB [auth I] Focus chain Z [auth B] Focus chain ZA [auth E] Focus chain ZD [auth P]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain BD [auth M] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GC [auth J] SDF format, chain ID [auth N] SDF format, chain JD [auth N] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain TD [auth P] SDF format, chain UC [auth L] SDF format, chain UD [auth P] SDF format, chain VC [auth L] SDF format, chain WB [auth I] SDF format, chain X [auth B] SDF format, chain XB [auth I] SDF format, chain AB [auth F] SDF format, chain CD [auth M] SDF format, chain FC [auth J] SDF format, chain HB [auth G] SDF format, chain IB [auth G] SDF format, chain NC [auth K] SDF format, chain OC [auth K] SDF format, chain PB [auth H] SDF format, chain QB [auth H] SDF format, chain Y [auth B] MOL2 format, chain BB [auth F] MOL2 format, chain BD [auth M] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GC [auth J] MOL2 format, chain ID [auth N] MOL2 format, chain JD [auth N] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain TD [auth P] MOL2 format, chain UC [auth L] MOL2 format, chain UD [auth P] MOL2 format, chain VC [auth L] MOL2 format, chain WB [auth I] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth I] MOL2 format, chain AB [auth F] MOL2 format, chain CD [auth M] MOL2 format, chain FC [auth J] MOL2 format, chain HB [auth G] MOL2 format, chain IB [auth G] MOL2 format, chain NC [auth K] MOL2 format, chain OC [auth K] MOL2 format, chain PB [auth H] MOL2 format, chain QB [auth H] MOL2 format, chain Y [auth B]	AB [auth F] BB [auth F] BD [auth M] CD [auth M] EA [auth C] AB [auth F], BB [auth F], BD [auth M], CD [auth M], EA [auth C], FA [auth C], FC [auth J], GC [auth J], HB [auth G], IB [auth G], ID [auth N], JD [auth N], LA [auth D], MA [auth D], NC [auth K], OC [auth K], PB [auth H], Q [auth A], QB [auth H], R [auth A], SA [auth E], TA [auth E], TD [auth P], UC [auth L], UD [auth P], VC [auth L], WB [auth I], X [auth B], XB [auth I], Y [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BB [auth F] Focus chain BD [auth M] Focus chain CD [auth M] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FC [auth J] Focus chain GC [auth J] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain ID [auth N] Focus chain JD [auth N] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NC [auth K] Focus chain OC [auth K] Focus chain PB [auth H] Focus chain Q [auth A] Focus chain QB [auth H] Focus chain R [auth A] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain TD [auth P] Focus chain UC [auth L] Focus chain UD [auth P] Focus chain VC [auth L] Focus chain WB [auth I] Focus chain X [auth B] Focus chain XB [auth I] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth F] Focus chain BB [auth F] Focus chain BD [auth M] Focus chain CD [auth M] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FC [auth J] Focus chain GC [auth J] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain ID [auth N] Focus chain JD [auth N] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NC [auth K] Focus chain OC [auth K] Focus chain PB [auth H] Focus chain Q [auth A] Focus chain QB [auth H] Focus chain R [auth A] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain TD [auth P] Focus chain UC [auth L] Focus chain UD [auth P] Focus chain VC [auth L] Focus chain WB [auth I] Focus chain X [auth B] Focus chain XB [auth I] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.252
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.486	α = 89.73
b = 151.14	β = 80.17
c = 160.319	γ = 71.64

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Morgan, H.P.

Walkinshaw, M.D.

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary