8SVM | pdb_00008svm

Plasmodium falciparum M17 aminopeptidase bound to MMV1557817

PDB DOI: https://doi.org/10.2210/pdb8SVM/pdb

Classification: HYDROLASE
Organism(s): Plasmodium falciparum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-05-17 Released: 2024-04-24
Deposition Author(s): McGowan, S., Drinkwater, N.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.252 (Depositor), 0.263 (DCC)
R-Value Work:
0.204 (Depositor), 0.218 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties.

de Koning-Ward, T.F., Drinkwater, N., Edgar, R.C.S., McGowan, S., Scammells, P.J.

(2024) mBio

Macromolecule Content

Total Structure Weight: 719.35 kDa
Atom Count: 50,860
Modeled Residue Count: 6,176
Deposited Residue Count: 6,336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine aminopeptidase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	528	Plasmodium falciparum	Mutation(s): 3 Gene Names: LAP, PF3D7_1446200 EC: 3.4.11.1 (PDB Primary Data), 3.4.13 (PDB Primary Data)
UniProt
Find proteins for Q8IL11 (Plasmodium falciparum (isolate 3D7)) Explore Q8IL11 Go to UniProtKB: Q8IL11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IL11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WRC (Subject of Investigation/LOI) Query on WRC Download:Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain EA [auth C] SDF format, chain EC [auth J] SDF format, chain IB [auth G] SDF format, chain LC [auth K] SDF format, chain NA [auth D] SDF format, chain P [auth A] SDF format, chain RB [auth H] SDF format, chain RC [auth L] SDF format, chain UA [auth E] SDF format, chain XB [auth I] SDF format, chain Y [auth B] MOL2 format, chain BB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain EC [auth J] MOL2 format, chain IB [auth G] MOL2 format, chain LC [auth K] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain RB [auth H] MOL2 format, chain RC [auth L] MOL2 format, chain UA [auth E] MOL2 format, chain XB [auth I] MOL2 format, chain Y [auth B] mmCIF format, chain BB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain EC [auth J] mmCIF format, chain IB [auth G] mmCIF format, chain LC [auth K] mmCIF format, chain NA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain RB [auth H] mmCIF format, chain RC [auth L] mmCIF format, chain UA [auth E] mmCIF format, chain XB [auth I] mmCIF format, chain Y [auth B]	BB [auth F] EA [auth C] EC [auth J] IB [auth G] LC [auth K] BB [auth F], EA [auth C], EC [auth J], IB [auth G], LC [auth K], NA [auth D], P [auth A], RB [auth H], RC [auth L], UA [auth E], XB [auth I], Y [auth B]	N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide C₂₀ H₂₁ F₃ N₂ O₃ NRAVUPOEFDEIOQ-GOSISDBHSA-N		Interactions Focus chain BB [auth F] Focus chain EA [auth C] Focus chain EC [auth J] Focus chain IB [auth G] Focus chain LC [auth K] Focus chain NA [auth D] Focus chain P [auth A] Focus chain RB [auth H] Focus chain RC [auth L] Focus chain UA [auth E] Focus chain XB [auth I] Focus chain Y [auth B] Interactions & Density Focus chain BB [auth F] Focus chain EA [auth C] Focus chain EC [auth J] Focus chain IB [auth G] Focus chain LC [auth K] Focus chain NA [auth D] Focus chain P [auth A] Focus chain RB [auth H] Focus chain RC [auth L] Focus chain UA [auth E] Focus chain XB [auth I] Focus chain Y [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AC [auth I] SDF format, chain CB [auth F] SDF format, chain DB [auth F] SDF format, chain FA [auth C] SDF format, chain FC [auth J] SDF format, chain GA [auth C] SDF format, chain GC [auth J] SDF format, chain HA [auth C] SDF format, chain JB [auth G] SDF format, chain KB [auth G] SDF format, chain MC [auth K] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SB [auth H] SDF format, chain SC [auth L] SDF format, chain TB [auth H] SDF format, chain TC [auth L] SDF format, chain UC [auth L] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain YB [auth I] SDF format, chain Z [auth B] SDF format, chain ZB [auth I] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth I] MOL2 format, chain CB [auth F] MOL2 format, chain DB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain FC [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain GC [auth J] MOL2 format, chain HA [auth C] MOL2 format, chain JB [auth G] MOL2 format, chain KB [auth G] MOL2 format, chain MC [auth K] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth H] MOL2 format, chain SC [auth L] MOL2 format, chain TB [auth H] MOL2 format, chain TC [auth L] MOL2 format, chain UC [auth L] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain YB [auth I] MOL2 format, chain Z [auth B] MOL2 format, chain ZB [auth I] mmCIF format, chain AA [auth B] mmCIF format, chain AC [auth I] mmCIF format, chain CB [auth F] mmCIF format, chain DB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain FC [auth J] mmCIF format, chain GA [auth C] mmCIF format, chain GC [auth J] mmCIF format, chain HA [auth C] mmCIF format, chain JB [auth G] mmCIF format, chain KB [auth G] mmCIF format, chain MC [auth K] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SB [auth H] mmCIF format, chain SC [auth L] mmCIF format, chain TB [auth H] mmCIF format, chain TC [auth L] mmCIF format, chain UC [auth L] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain YB [auth I] mmCIF format, chain Z [auth B] mmCIF format, chain ZB [auth I]	AA [auth B] AC [auth I] CB [auth F] DB [auth F] FA [auth C] AA [auth B], AC [auth I], CB [auth F], DB [auth F], FA [auth C], FC [auth J], GA [auth C], GC [auth J], HA [auth C], JB [auth G], KB [auth G], MC [auth K], OA [auth D], PA [auth D], Q [auth A], R [auth A], S [auth A], SB [auth H], SC [auth L], TB [auth H], TC [auth L], UC [auth L], VA [auth E], WA [auth E], XA [auth E], YB [auth I], Z [auth B], ZB [auth I]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AC [auth I] Focus chain CB [auth F] Focus chain DB [auth F] Focus chain FA [auth C] Focus chain FC [auth J] Focus chain GA [auth C] Focus chain GC [auth J] Focus chain HA [auth C] Focus chain JB [auth G] Focus chain KB [auth G] Focus chain MC [auth K] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SB [auth H] Focus chain SC [auth L] Focus chain TB [auth H] Focus chain TC [auth L] Focus chain UC [auth L] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YB [auth I] Focus chain Z [auth B] Focus chain ZB [auth I] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth I] Focus chain CB [auth F] Focus chain DB [auth F] Focus chain FA [auth C] Focus chain FC [auth J] Focus chain GA [auth C] Focus chain GC [auth J] Focus chain HA [auth C] Focus chain JB [auth G] Focus chain KB [auth G] Focus chain MC [auth K] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SB [auth H] Focus chain SC [auth L] Focus chain TB [auth H] Focus chain TC [auth L] Focus chain UC [auth L] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YB [auth I] Focus chain Z [auth B] Focus chain ZB [auth I]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain EB [auth F] SDF format, chain HC [auth J] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain LB [auth G] SDF format, chain MB [auth G] SDF format, chain NB [auth G] SDF format, chain NC [auth K] SDF format, chain QA [auth D] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain VC [auth L] MOL2 format, chain EB [auth F] MOL2 format, chain HC [auth J] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain LB [auth G] MOL2 format, chain MB [auth G] MOL2 format, chain NB [auth G] MOL2 format, chain NC [auth K] MOL2 format, chain QA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain VC [auth L] mmCIF format, chain EB [auth F] mmCIF format, chain HC [auth J] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain LB [auth G] mmCIF format, chain MB [auth G] mmCIF format, chain NB [auth G] mmCIF format, chain NC [auth K] mmCIF format, chain QA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain VC [auth L]	EB [auth F] HC [auth J] IA [auth C] JA [auth C] LB [auth G] EB [auth F], HC [auth J], IA [auth C], JA [auth C], LB [auth G], MB [auth G], NB [auth G], NC [auth K], QA [auth D], T [auth A], U [auth A], VC [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EB [auth F] Focus chain HC [auth J] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain LB [auth G] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain NC [auth K] Focus chain QA [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain VC [auth L] Interactions & Density Focus chain EB [auth F] Focus chain HC [auth J] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain LB [auth G] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain NC [auth K] Focus chain QA [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain VC [auth L]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain CA [auth C] SDF format, chain CC [auth J] SDF format, chain DA [auth C] SDF format, chain DC [auth J] SDF format, chain GB [auth G] SDF format, chain HB [auth G] SDF format, chain JC [auth K] SDF format, chain KC [auth K] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain PB [auth H] SDF format, chain PC [auth L] SDF format, chain QB [auth H] SDF format, chain QC [auth L] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain VB [auth I] SDF format, chain W [auth B] SDF format, chain WB [auth I] SDF format, chain X [auth B] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain CC [auth J] MOL2 format, chain DA [auth C] MOL2 format, chain DC [auth J] MOL2 format, chain GB [auth G] MOL2 format, chain HB [auth G] MOL2 format, chain JC [auth K] MOL2 format, chain KC [auth K] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PB [auth H] MOL2 format, chain PC [auth L] MOL2 format, chain QB [auth H] MOL2 format, chain QC [auth L] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain VB [auth I] MOL2 format, chain W [auth B] MOL2 format, chain WB [auth I] MOL2 format, chain X [auth B] MOL2 format, chain ZA [auth F] mmCIF format, chain AB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain CC [auth J] mmCIF format, chain DA [auth C] mmCIF format, chain DC [auth J] mmCIF format, chain GB [auth G] mmCIF format, chain HB [auth G] mmCIF format, chain JC [auth K] mmCIF format, chain KC [auth K] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain PB [auth H] mmCIF format, chain PC [auth L] mmCIF format, chain QB [auth H] mmCIF format, chain QC [auth L] mmCIF format, chain SA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain VB [auth I] mmCIF format, chain W [auth B] mmCIF format, chain WB [auth I] mmCIF format, chain X [auth B] mmCIF format, chain ZA [auth F]	AB [auth F] CA [auth C] CC [auth J] DA [auth C] DC [auth J] AB [auth F], CA [auth C], CC [auth J], DA [auth C], DC [auth J], GB [auth G], HB [auth G], JC [auth K], KC [auth K], LA [auth D], MA [auth D], N [auth A], O [auth A], PB [auth H], PC [auth L], QB [auth H], QC [auth L], SA [auth E], TA [auth E], VB [auth I], W [auth B], WB [auth I], X [auth B], ZA [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain CA [auth C] Focus chain CC [auth J] Focus chain DA [auth C] Focus chain DC [auth J] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain JC [auth K] Focus chain KC [auth K] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain PB [auth H] Focus chain PC [auth L] Focus chain QB [auth H] Focus chain QC [auth L] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain VB [auth I] Focus chain W [auth B] Focus chain WB [auth I] Focus chain X [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain CA [auth C] Focus chain CC [auth J] Focus chain DA [auth C] Focus chain DC [auth J] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain JC [auth K] Focus chain KC [auth K] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain PB [auth H] Focus chain PC [auth L] Focus chain QB [auth H] Focus chain QC [auth L] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain VB [auth I] Focus chain W [auth B] Focus chain WB [auth I] Focus chain X [auth B] Focus chain ZA [auth F]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain BC [auth J] SDF format, chain FB [auth G] SDF format, chain IC [auth K] SDF format, chain KA [auth D] SDF format, chain M [auth A] SDF format, chain OB [auth H] SDF format, chain OC [auth L] SDF format, chain RA [auth E] SDF format, chain UB [auth I] SDF format, chain V [auth B] SDF format, chain YA [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain BC [auth J] MOL2 format, chain FB [auth G] MOL2 format, chain IC [auth K] MOL2 format, chain KA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain OB [auth H] MOL2 format, chain OC [auth L] MOL2 format, chain RA [auth E] MOL2 format, chain UB [auth I] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain BC [auth J] mmCIF format, chain FB [auth G] mmCIF format, chain IC [auth K] mmCIF format, chain KA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain OB [auth H] mmCIF format, chain OC [auth L] mmCIF format, chain RA [auth E] mmCIF format, chain UB [auth I] mmCIF format, chain V [auth B] mmCIF format, chain YA [auth F]	BA [auth C] BC [auth J] FB [auth G] IC [auth K] KA [auth D] BA [auth C], BC [auth J], FB [auth G], IC [auth K], KA [auth D], M [auth A], OB [auth H], OC [auth L], RA [auth E], UB [auth I], V [auth B], YA [auth F]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain BC [auth J] Focus chain FB [auth G] Focus chain IC [auth K] Focus chain KA [auth D] Focus chain M [auth A] Focus chain OB [auth H] Focus chain OC [auth L] Focus chain RA [auth E] Focus chain UB [auth I] Focus chain V [auth B] Focus chain YA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain BC [auth J] Focus chain FB [auth G] Focus chain IC [auth K] Focus chain KA [auth D] Focus chain M [auth A] Focus chain OB [auth H] Focus chain OC [auth L] Focus chain RA [auth E] Focus chain UB [auth I] Focus chain V [auth B] Focus chain YA [auth F]