6CJ9 | pdb_00006cj9

Crystal structure of lectin from Dioclea lasiophylla seeds (DlyL) complexed with X-Man

• PDB DOI: https://doi.org/10.2210/pdb6CJ9/pdb
• Entry: 6CJ9 supersedes: 5U37

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Dioclea lasiophylla
• Mutation(s): No 


• Deposited: 2018-02-26 Released: 2018-03-07 
• Deposition Author(s): Pinto-Junior, V.R., Santiago, M.Q., Osterne, V.J.S., Araripe, D.A., Neco, A.H.B., Silva-Filho, J.C., Leal, R.B., Rocha, C.R.C., Nascimento, K.S., Cavada, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DlyL, a mannose-specific lectin from Dioclea lasiophylla Mart. Ex Benth seeds that display cytotoxic effects against C6 glioma cells.

Leal, R.B., Pinto-Junior, V.R., Osterne, V.J.S., Wolin, I.A.V., Nascimento, A.P.M., Neco, A.H.B., Araripe, D.A., Welter, P.G., Neto, C.C., Correia, J.L.A., Rocha, C.R.C., Nascimento, K.S., Cavada, B.S.

(2018) Int J Biol Macromol 114: 64-76

• PubMed: 29559315 
• DOI: https://doi.org/10.1016/j.ijbiomac.2018.03.080
• Primary Citation Related Structures: 
  6CJ9

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Organizational Affiliation: 
• Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil.
Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil.
Universidade Federal de Pernambuco (UFPE), Pernambuco, Recife, Brazil.
Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 25.92 kDa 
• Atom Count: 2,072 
• Modeled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A	237	Dioclea lasiophylla	Mutation(s): 0
UniProt
Find proteins for C0HK27 (Dioclea lasiophylla) Explore C0HK27  Go to UniProtKB:  C0HK27

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XMM	D [auth A]	5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside C14 H15 Br Cl N O6 OPIFSICVWOWJMJ-HAAGFXOZSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.1	α = 90
b = 86.93	β = 90
c = 92.82	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Pinto-Junior, V.R., Santiago, M.Q., Osterne, V.J.S., Araripe, D.A., Neco, A.H.B., Silva-Filho, J.C., Leal, R.B., Rocha, C.R.C., Nascimento, K.S., Cavada, B.S.
• This entry supersedes: 5U37

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary