3HP8

Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG, bound to sucrose

• PDB DOI: https://doi.org/10.2210/pdb3HP8/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Tuber borchii, Neurospora crassa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-03 Released: 2009-06-23 
• Deposition Author(s): Koharudin, L.M.I., Furey, W., Gronenborn, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.277 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.45 kDa 
• Atom Count: 2,067 
• Modelled Residue Count: 214 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanovirin-N-like protein	A, B	110	Tuber borchii, Neurospora crassa	Mutation(s): 0
UniProt
Find proteins for Q5MK11 (Tuber borchii) Explore Q5MK11  Go to UniProtKB:  Q5MK11
Find proteins for Q7S6U4 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q7S6U4  Go to UniProtKB:  Q7S6U4
UniProt Groups	Q5MK11Q7S6U4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D, E, F	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	G [auth A], H [auth B]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C, D, E, F	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.277 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.497	α = 90
b = 39.298	β = 97.64
c = 86.134	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Koharudin, L.M.I., Furey, W., Gronenborn, A.M.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary