8RDC | pdb_00008rdc

Galectin-1 in complex with thiogalactoside derivative

PDB DOI: https://doi.org/10.2210/pdb8RDC/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-07 Released: 2024-12-18
Deposition Author(s): Hakansson, M., Diehl, C., Peterson, K., Zetterberg, F., Nilsson, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.200 (Depositor), 0.208 (DCC)
R-Value Work:
0.172 (Depositor), 0.184 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Galectin-1 in complex with thiogalactoside derivative

Hakansson, M., Diehl, C., Petersn, K., Nilsson, U.

To be published.

Macromolecule Content

Total Structure Weight: 31.69 kDa
Atom Count: 2,455
Modeled Residue Count: 268
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	A, B	135	Homo sapiens	Mutation(s): 0 Gene Names: LGALS1
UniProt & NIH Common Fund Data Resources
Find proteins for P09382 (Homo sapiens) Explore P09382 Go to UniProtKB: P09382
PHAROS: P09382 GTEx: ENSG00000100097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09382
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YNO (Subject of Investigation/LOI) Query on YNO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	5-bromanyl-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-4-[4-(4-chloranyl-1,3-thiazol-2-yl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3-methoxy-5-oxidanyl-oxan-2-yl]sulfanyl-pyridine-2-carbonitrile C₁₈ H₁₆ Br Cl N₆ O₄ S₂ MZSZXCMHHUHYMW-PTERYMMESA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	D [auth A], E [auth A], F [auth A], G [auth A], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]