3DWS

Leishmania major Coproporphyrinogen III Oxidase with bound ligand

PDB DOI: https://doi.org/10.2210/pdb3DWS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leishmania major
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-22 Released: 2008-09-09
Deposition Author(s): Le Trong, I., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259
R-Value Work: 0.161
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Leishmania major Coproporphyrinogen III Oxidase with bound ligand

merritt, E.A., Le Trong, I., Larson, E.T., Shibata, S., Zhang, Z., Anderson, L., Ross, J., Deng, W., Verlinde, C.L.M.J., Buckner, F.S., Van Voorhis, W.C., Hol, W.G.J., Fan, E.

To be published.

Macromolecule Content

Total Structure Weight: 71.98 kDa
Atom Count: 5,547
Modelled Residue Count: 606
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproporphyrinogen III oxidase	A, B	309	Leishmania major	Mutation(s): 0 Gene Names: LMAJ006828, LmjF06.1270 EC: 1.3.3.3
UniProt
Find proteins for P84155 (Leishmania major) Explore P84155 Go to UniProtKB: P84155
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84155
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FIC Query on FIC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	5-fluoroindole-2-carboxylic acid C₉ H₆ F N O₂ WTXBRZCVLDTWLP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], E [auth B], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259
R-Value Work: 0.161
R-Value Observed: 0.166
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.075	α = 86.22
b = 53.625	β = 77.37
c = 65.599	γ = 61.08

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Le Trong, I.

Merritt, E.A.

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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3DWS

Leishmania major Coproporphyrinogen III Oxidase with bound ligand

Leishmania major Coproporphyrinogen III Oxidase with bound ligand

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)