3NAK | pdb_00003nak

Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite at 3.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb3NAK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Capra hircus
Mutation(s): No

Deposited: 2010-06-02 Released: 2010-07-28
Deposition Author(s): Vikram, G., Singh, R.P., Singh, A.K., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.243 (Depositor), 0.281 (DCC)
R-Value Work:
0.205 (Depositor), 0.208 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite at 3.3 A resolution

Vikram, G., Singh, R.P., Singh, A.K., Sinha, M., Bhushan, A., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 141.24 kDa
Atom Count: 10,098
Modeled Residue Count: 1,190
Deposited Residue Count: 1,190
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A, B	595	Capra hircus	Mutation(s): 0 EC: 1.11.1.7
UniProt
Find proteins for A0A452E9Y6 (Capra hircus) Explore A0A452E9Y6 Go to UniProtKB: A0A452E9Y6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A452E9Y6
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, G	3		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain G Interactions & Density Focus chain C Focus chain D Focus chain G
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

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)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, I	3		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain I Interactions & Density Focus chain E Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth A]	L [auth A], Q [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B]
OSM Query on OSM Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A]	M [auth A], R [auth B]	1-(OXIDOSULFANYL)METHANAMINE C H₅ N O S KONFWJXIYYGXOO-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain R [auth B] Interactions & Density Focus chain M [auth A] Focus chain R [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A], S [auth B], T [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A]	K [auth A], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain P [auth B] Interactions & Density Focus chain K [auth A] Focus chain P [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.243 (Depositor), 0.281 (DCC)
R-Value Work: 0.205 (Depositor), 0.208 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.991	α = 85.45
b = 72.272	β = 84.04
c = 83.652	γ = 75.89

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary