4MX2 | pdb_00004mx2

Crystal Structure of adenylosuccinate lyase from Leishmania donovani

PDB DOI: https://doi.org/10.2210/pdb4MX2/pdb

Classification: LYASE
Organism(s): Leishmania donovani
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-09-25 Released: 2014-04-16
Deposition Author(s): Wernimont, A.K., Loppnau, P., Dong, A., Krojer, T., Bradley, A., Bushell, S., von Delft, F., Robinson, D., Gilbert, I., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Mottaghi, K., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.253 (Depositor), 0.262 (DCC)
R-Value Work:
0.218 (Depositor), 0.226 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of adenylosuccinate lyase from Leishmania donovani

Wernimont, A.K., Loppnau, P., Dong, A., Krojer, T., Bradley, A., Bushell, S., von Delft, F., Robinson, D., Gilbert, I., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Mottaghi, K.

To be published.

Macromolecule Content

Total Structure Weight: 432.53 kDa
Atom Count: 29,460
Modeled Residue Count: 3,449
Deposited Residue Count: 3,840
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate lyase	A, B, C, D, E A, B, C, D, E, F, G, H	480	Leishmania donovani	Mutation(s): 0 Gene Names: ASL, LdBPK_040440.1 EC: 4.3.2.2
UniProt
Find proteins for A7LBL3 (Leishmania donovani) Explore A7LBL3 Go to UniProtKB: A7LBL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7LBL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain S [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain S [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain S [auth H]	I [auth A] J [auth B] K [auth C] M [auth D] O [auth E] I [auth A], J [auth B], K [auth C], M [auth D], O [auth E], P [auth F], Q [auth G], S [auth H]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain S [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain S [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain R [auth G] SDF format, chain T [auth H] MOL2 format, chain L [auth C] MOL2 format, chain R [auth G] MOL2 format, chain T [auth H] mmCIF format, chain L [auth C] mmCIF format, chain R [auth G] mmCIF format, chain T [auth H]	L [auth C], R [auth G], T [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth C] Focus chain R [auth G] Focus chain T [auth H] Interactions & Density Focus chain L [auth C] Focus chain R [auth G] Focus chain T [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth E] MOL2 format, chain N [auth E] mmCIF format, chain N [auth E]	N [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth E] Interactions & Density Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.253 (Depositor), 0.262 (DCC)
R-Value Work: 0.218 (Depositor), 0.226 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.015	α = 90
b = 194.697	β = 91.31
c = 147.507	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
Aimless	data scaling
BALBES	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-16

Deposition Author(s):

Wernimont, A.K.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-04-16
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.