3AFK

Crystal Structure of Agrocybe aegerita lectin AAL complexed with Thomsen-Friedenreich antigen

PDB DOI: https://doi.org/10.2210/pdb3AFK/pdb

Classification: HYDROLASE
Organism(s): Cyclocybe aegerita
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-09 Released: 2010-12-01
Deposition Author(s): Feng, L., Li, D., Wang, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.219
R-Value Work: 0.186

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 37.37 kDa
Atom Count: 2,918
Modelled Residue Count: 333
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-tumor lectin	A, B	167	Cyclocybe aegerita	Mutation(s): 0 Gene Names: AAL EC: 3.1.21
UniProt
Find proteins for Q6WY08 (Cyclocybe aegerita) Explore Q6WY08 Go to UniProtKB: Q6WY08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6WY08
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	C, D	2		O-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G00031MO GlyCosmos: G00031MO GlyGen: G00031MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THR Query on THR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	THREONINE C₄ H₉ N O₃ AYFVYJQAPQTCCC-GBXIJSLDSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084 Query on PRD_900084	C, D	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.219
R-Value Work: 0.186
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.85	α = 102.08
b = 43.44	β = 98.15
c = 56.06	γ = 118.06

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Feng, L.

Li, D.

Wang, D.

Revision History (Full details and data files)

Version 1.0: 2010-12-01
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, Database references, Derived calculations, Structure summary
Version 2.1: 2024-03-13
Changes: Data collection, Database references, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3AFK

Crystal Structure of Agrocybe aegerita lectin AAL complexed with Thomsen-Friedenreich antigen

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)