4A5G | pdb_00004a5g

Raphanus sativus anionic peroxidase.

PDB DOI: https://doi.org/10.2210/pdb4A5G/pdb

Classification: OXIDOREDUCTASE
Organism(s): Raphanus sativus
Mutation(s): No

Deposited: 2011-10-25 Released: 2012-11-07
Deposition Author(s): Jimenez-Arroyo, N., Valderrama, B., Gil-Rodriguez, P., Rojas-Trejo, S.P., Rudino-Pinera, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.185 (Depositor), 0.181 (DCC)
R-Value Work:
0.163 (Depositor), 0.157 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystallographic Structure of the Raphanus Sativus Anionic Peroxidase

Gil-Rodriguez, P., Jimenez-Arroyo, N., Rojas-Trejo, S.P., Rudino-Pinera, E., Valderrama, B.

To be published.

Macromolecule Content

Total Structure Weight: 75.74 kDa
Atom Count: 5,969
Modeled Residue Count: 614
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANIONIC PEROXIDASE	A, B	308	Raphanus sativus	Mutation(s): 0 EC: 1.11.1.7
UniProt
Find proteins for K7N5L9 (Raphanus sativus) Explore K7N5L9 Go to UniProtKB: K7N5L9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K7N5L9
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, I	6		N-Glycosylation	Interactions Focus chain C Focus chain I Interactions & Density Focus chain C Focus chain I
Glycosylation Resources
GlyTouCan: G68461PT GlyCosmos: G68461PT GlyGen: G68461PT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G18638YB GlyCosmos: G18638YB GlyGen: G18638YB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G58582QS GlyCosmos: G58582QS GlyGen: G58582QS

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	F, L	4		N-Glycosylation	Interactions Focus chain F Focus chain L Interactions & Density Focus chain F Focus chain L
Glycosylation Resources
GlyTouCan: G73622RM GlyCosmos: G73622RM GlyGen: G73622RM

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	6		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G62684SI GlyCosmos: G62684SI GlyGen: G62684SI

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	2		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	4		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G77577HJ GlyCosmos: G77577HJ GlyGen: G77577HJ

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	K	3		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain S [auth B] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B]	M [auth A], S [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain M [auth A] Focus chain S [auth B] Interactions & Density Focus chain M [auth A] Focus chain S [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain Q [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain R [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain R [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain R [auth A]	BA [auth B] CA [auth B] DA [auth B] Q [auth A] R [auth A] BA [auth B], CA [auth B], DA [auth B], Q [auth A], R [auth A], Y [auth B], Z [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain V [auth B] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain V [auth B] mmCIF format, chain P [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain V [auth B]	P [auth A], V [auth B], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	N [auth A], O [auth A], T [auth B], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.185 (Depositor), 0.181 (DCC)
R-Value Work: 0.163 (Depositor), 0.157 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.148	α = 90
b = 41.192	β = 96.91
c = 137.796	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2013-01-16
Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary