4NO4 | pdb_00004no4

Crystal Structure of Galectin-1 L11A mutant

PDB DOI: https://doi.org/10.2210/pdb4NO4/pdb

Classification: APOPTOSIS
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-11-19 Released: 2014-12-03
Deposition Author(s): Dessau, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Galectin-1 L11A mutant

Dessau, M., Segev, O.

To be published.

Macromolecule Content

Total Structure Weight: 91.07 kDa
Atom Count: 7,753
Modeled Residue Count: 804
Deposited Residue Count: 804
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, C, D, E A, B, C, D, E, F	134	Rattus norvegicus	Mutation(s): 1 Gene Names: Lgals1
UniProt
Find proteins for P11762 (Rattus norvegicus) Explore P11762 Go to UniProtKB: P11762
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11762
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L	2		N/A	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain N [auth A] MOL2 format, chain T [auth E] MOL2 format, chain N [auth A] mmCIF format, chain T [auth E] mmCIF format, chain N [auth A]	N [auth A], T [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth A] Focus chain T [auth E] Interactions & Density Focus chain N [auth A] Focus chain T [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A] P [auth A] Q [auth B] S [auth C] U [auth E] O [auth A], P [auth A], Q [auth B], S [auth C], U [auth E], W [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth E] Focus chain W [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain R [auth C] SDF format, chain M [auth A] MOL2 format, chain V [auth F] MOL2 format, chain R [auth C] MOL2 format, chain M [auth A] mmCIF format, chain V [auth F] mmCIF format, chain R [auth C] mmCIF format, chain M [auth A]	M [auth A], R [auth C], V [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain R [auth C] Focus chain V [auth F] Interactions & Density Focus chain M [auth A] Focus chain R [auth C] Focus chain V [auth F]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004 Query on PRD_900004	G, H, I, J, K G, H, I, J, K, L	beta-lactose	Oligosaccharide / Nutrient		Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.52	α = 90
b = 193.83	β = 90
c = 108.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Dessau, M.

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-02-28
Changes: Data collection, Database references, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

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Crystal Structure of Galectin-1 L11A mutant

Crystal Structure of Galectin-1 L11A mutant

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)

4NO4 | pdb_00004no4