1ONK

Mistletoe lectin I from viscum album

PDB DOI: https://doi.org/10.2210/pdb1ONK/pdb

Classification: hydrolase/sugar binding protein
Organism(s): Viscum album
Mutation(s): No

Deposited: 2003-02-28 Released: 2004-02-28
Deposition Author(s): Gabdoulkhakov, A.G., Savoshkina, Y., Krauspenhaar, R., Stoeva, S., Konareva, N., Kornilov, V., Kornev, A.N., Voelter, W., Nikonov, S.V., Betzel, C., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223
R-Value Work: 0.160
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 59.1 kDa
Atom Count: 4,453
Modelled Residue Count: 512
Deposited Residue Count: 517
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactoside specific lectin I A chain	A	254	Viscum album	Mutation(s): 0 EC: 3.2.2.22
UniProt
Find proteins for P81446 (Viscum album) Explore P81446 Go to UniProtKB: P81446
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81446
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose specific lectin I B chain	B	263	Viscum album	Mutation(s): 0
UniProt
Find proteins for P81446 (Viscum album) Explore P81446 Go to UniProtKB: P81446
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81446
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], T [auth B], U [auth B], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth B] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain R [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] O [auth B] D [auth A], E [auth A], F [auth A], G [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223
R-Value Work: 0.160
R-Value Observed: 0.163
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.285	α = 90
b = 107.285	β = 90
c = 311.773	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-02-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-02-28
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary