2XF2

PVC-AT

PDB DOI: https://doi.org/10.2210/pdb2XF2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Penicillium janthinellum
Mutation(s): No

Deposited: 2010-05-20 Released: 2010-06-16
Deposition Author(s): Borovik, A., Melik-Adamyan, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.173
R-Value Work: 0.149
R-Value Observed: 0.150

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

X-Ray Investigation of Penicillium Vitale Catalase Inhibited by Aminotriazole

Borovik, A., Grebenko, A.I., Melik-Adamyan, W.R.

(2011) Crystallogr Rep 56: 590

DOI: https://doi.org/10.1134/S1063774511030060

Macromolecule Content

Total Structure Weight: 154.01 kDa
Atom Count: 11,955
Modelled Residue Count: 1,376
Deposited Residue Count: 1,376
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALASE	A, B [auth E]	688	Penicillium janthinellum	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for D9N167 (Penicillium janthinellum) Explore D9N167 Go to UniProtKB: D9N167
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D9N167
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B [auth E]
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HDD Query on HDD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth E] MOL2 format, chain C [auth A] MOL2 format, chain K [auth E] mmCIF format, chain C [auth A] mmCIF format, chain K [auth E]	C [auth A], K [auth E]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C₃₄ H₃₂ Fe N₄ O₅ UMGOPAWIGKFTRK-QQDQPIDJSA-N		Interactions Focus chain C [auth A] Focus chain K [auth E] Interactions & Density Focus chain C [auth A] Focus chain K [auth E]
NAG Query on NAG 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 L [auth E] SDF format, chain M [auth E] SDF format, chain N [auth E] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth E] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E]	D [auth A] E [auth A] F [auth A] L [auth E] M [auth E] D [auth A], E [auth A], F [auth A], L [auth E], M [auth E], N [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E]
3TR Query on 3TR Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain O [auth E]	G [auth A], O [auth E]	3-AMINO-1,2,4-TRIAZOLE C₂ H₄ N₄ KLSJWNVTNUYHDU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain O [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain R [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E]	H [auth A] I [auth A] J [auth A] P [auth E] Q [auth E] H [auth A], I [auth A], J [auth A], P [auth E], Q [auth E], R [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.173
R-Value Work: 0.149
R-Value Observed: 0.150
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.3	α = 90
b = 144.3	β = 90
c = 133.8	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-06-16

Deposition Author(s):

Borovik, A.

Melik-Adamyan, W.R.

Revision History (Full details and data files)

Version 1.0: 2010-06-16
Type: Initial release
Version 1.1: 2011-08-24
Changes: Non-polymer description, Other, Version format compliance
Version 1.2: 2014-02-05
Changes: Data collection, Database references
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations
Version 1.4: 2019-10-16
Changes: Data collection, Experimental preparation, Other
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.6: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.7: 2024-11-06
Changes: Structure summary