8VCS

Crystal structure of the oligomeric rMcL-1 in complex with lactose

PDB DOI: https://doi.org/10.2210/pdb8VCS/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Mytilus californianus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-12-14 Released: 2024-12-18
Deposition Author(s): Hernandez-Santoyo, A., Loera-Rubalcava, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.188 (Depositor), 0.191 (DCC)
R-Value Work:
0.167 (Depositor), 0.171 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Insights into a mytilectin from Mytilus californianus: Study of its unique galactoside interactions, oligomerization patterns, and antifungal activity

Loera-Rubalcava, J., Garcia-Maldonado, E., Cano-Sanchez, P., Rodriguez-Romero, A., Quintero-Martinez, A., Macias-Rubalcava, M.L., Espinosa-Perez, G., Hernandez-Santoyo, A.

To be published.

Macromolecule Content

Total Structure Weight: 143.77 kDa
Atom Count: 10,807
Modelled Residue Count: 1,203
Deposited Residue Count: 1,216
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-binding lectin	A, B, C, D, E A, B, C, D, E, F, G, H	152	Mytilus californianus	Mutation(s): 3
UniProt
Find proteins for A0A0P0E482 (Mytilus californianus) Explore A0A0P0E482 Go to UniProtKB: A0A0P0E482
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0P0E482
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T]	2		N/A	Interactions Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth S] Focus chain S [auth T] Interactions & Density Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth S] Focus chain S [auth T]
Glycosylation Resources
GlyTouCan: G88362QR GlyCosmos: G88362QR GlyGen: G88362QR

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL (Subject of Investigation/LOI) Query on GAL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth F] BA [auth F] CA [auth F] DA [auth G] FA [auth H] AA [auth F], BA [auth F], CA [auth F], DA [auth G], FA [auth H], T [auth A], U [auth A], V [auth B], W [auth C], X [auth C], Y [auth D], Z [auth D]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain EA [auth G] MOL2 format, chain EA [auth G] mmCIF format, chain EA [auth G]	EA [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Interactions & Density Focus chain EA [auth G]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008 Query on PRD_900008	I [auth J] J [auth K] K [auth L] L [auth M] M [auth N] I [auth J], J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T]	alpha-lactose	Oligosaccharide / Nutrient		Interactions Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth S] Focus chain S [auth T] Interactions & Density Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth S] Focus chain S [auth T]