1ONK | pdb_00001onk

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.223 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Mistletoe lectin I from viscum album

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.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA,PQS (software)

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

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 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
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	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
AZI	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.223 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• 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
• Version 1.5: 2024-11-13
  Changes: Structure summary