3NIU | pdb_00003niu

Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 A resolution

PDB DOI: https://doi.org/10.2210/pdb3NIU/pdb

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

Deposited: 2010-06-16 Released: 2010-07-14
Deposition Author(s): Vikram, G., Singh, R.P., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free:
0.232 (Depositor), 0.270 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 140.44 kDa
Atom Count: 10,318
Modeled Residue Count: 1,190
Deposited Residue Count: 1,190
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E, F, G	2		N-Glycosylation	Interactions Focus chain C Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain C Focus chain E Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, H	3		N-Glycosylation	Interactions Focus chain D Focus chain H Interactions & Density Focus chain D Focus chain H
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B]	I [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B]	N [auth A], T [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain T [auth B] Interactions & Density Focus chain N [auth A] Focus chain T [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	J [auth A], K [auth A], P [auth B], Q [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B]	L [auth A], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain R [auth B] Interactions & Density Focus chain L [auth A] Focus chain R [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: 2.94 Å
R-Value Free: 0.232 (Depositor), 0.270 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.199	α = 79.93
b = 75.587	β = 77.86
c = 83.808	γ = 72.5

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: 2010-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-14
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: 2024-11-13
Changes: Structure summary

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Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 A resolution

Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 A resolution

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3NIU | pdb_00003niu