6CJ9

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.215
R-Value Work: 0.183
R-Value Observed: 0.185

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.ijbiomac.2018.03.080
Primary Citation of Related Structures:
6CJ9

Organizational Affiliation

Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C0HK27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XMM Query on XMM Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside C₁₄ H₁₅ Br Cl N O₆ OPIFSICVWOWJMJ-HAAGFXOZSA-N		Interactions Focus chain D [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.215
R-Value Work: 0.183
R-Value Observed: 0.185
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

This entry supersedes: 5U37

Revision History (Full details and data files)

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