4JN0 | pdb_00004jn0

Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 1H-pyrrolo[3,2-b]pyridine-6-carbaldehyde

PDB DOI: https://doi.org/10.2210/pdb4JN0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae RM11-1a
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-03-14 Released: 2013-05-01
Deposition Author(s): Barelier, S., Fischer, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.194 (Depositor), 0.192 (DCC)
R-Value Work:
0.150 (Depositor), 0.148 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4JN0

Ligand Structure Quality Assessment

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

Literature

Docking to a water-filled model binding site in Cytochrome c Peroxidase

Barelier, S., Boyce, S.E., Fish, I., Fischer, M., Goodin, D.B., Shoichet, B.K.

To be published.

Macromolecule Content

Total Structure Weight: 33.69 kDa
Atom Count: 2,843
Modeled Residue Count: 289
Deposited Residue Count: 289
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c peroxidase	A	289	Saccharomyces cerevisiae RM11-1a	Mutation(s): 2 Gene Names: CCP1 CCP CPO YKR066C, SCRG_04081 EC: 1.11.1.5 (PDB Primary Data), 1.11.1 (UniProt)
UniProt
Find proteins for B3LRE1 (Saccharomyces cerevisiae (strain RM11-1a)) Explore B3LRE1 Go to UniProtKB: B3LRE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3LRE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
1MJ Query on 1MJ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1H-pyrrolo[3,2-b]pyridine-6-carbaldehyde C₈ H₆ N₂ O HRLUESWIQOAEBQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.194 (Depositor), 0.192 (DCC)
R-Value Work: 0.150 (Depositor), 0.148 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.07	α = 90
b = 74.56	β = 90
c = 50.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-05-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-01
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.