7DES | pdb_00007des

Acyl-Coenzyme A Binding Protein 103 (LMJF_17_0620) of Leishmania Major

PDB DOI: https://doi.org/10.2210/pdb7DES/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Leishmania major
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-11-04 Released: 2022-05-04
Deposition Author(s): Verma, S., Sundd, M., Makde, R.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.194 (Depositor), 0.194 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Acyl-Coenzyme A Binding Protein 103 (LMJF_17_0620) of Leishmania Major

Verma, S., Sundd, M., Makde, R.D.

To be published.

Macromolecule Content

Total Structure Weight: 11.6 kDa
Atom Count: 855
Modeled Residue Count: 96
Deposited Residue Count: 103
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACB domain-containing protein	A	103	Leishmania major	Mutation(s): 0 Gene Names: LMJF_17_0620
UniProt
Find proteins for Q4QED2 (Leishmania major) Explore Q4QED2 Go to UniProtKB: Q4QED2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4QED2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT (Subject of Investigation/LOI) Query on FMT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.194 (Depositor), 0.194 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.946	α = 90
b = 36.996	β = 104.016
c = 58.611	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.