5C4Q

Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine

PDB DOI: https://doi.org/10.2210/pdb5C4Q/pdb

Classification: TRANSCRIPTION
Organism(s): Leishmania donovani BPK282A1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-06-18 Released: 2015-07-08
Deposition Author(s): Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Amani, M., Hou, C.F.D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.240
R-Value Work: 0.181
R-Value Observed: 0.184

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine

Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Amani, M., Hou, C.F.D.

To be published.

Macromolecule Content

Total Structure Weight: 29.69 kDa
Atom Count: 2,071
Modelled Residue Count: 232
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain	A, B	125	Leishmania donovani BPK282A1	Mutation(s): 0 Gene Names: LDBPK_363130
UniProt
Find proteins for A0A3Q8IW45 (Leishmania donovani) Explore A0A3Q8IW45 Go to UniProtKB: A0A3Q8IW45
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3Q8IW45
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BMF Query on BMF Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	Bromosporine C₁₇ H₂₀ N₆ O₄ S UYBRROMMFMPJAN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.240
R-Value Work: 0.181
R-Value Observed: 0.184
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.916	α = 90
b = 34.385	β = 117.58
c = 86.463	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-08

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2015-07-08
Type: Initial release
Version 1.1: 2017-11-01
Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description