8VCU

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

PDB DOI: https://doi.org/10.2210/pdb8VCU/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: 1.77 Å
R-Value Free: 0.229
R-Value Work: 0.185
R-Value Observed: 0.186

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 74.81 kDa
Atom Count: 5,820
Modelled Residue Count: 597
Deposited Residue Count: 608
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	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

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose	E [auth G], F [auth H], G [auth I], H [auth J], I [auth K], E [auth G], F [auth H], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U], T [auth V]	2		N/A	Interactions Focus chain E [auth G] Focus chain F [auth H] Focus chain G [auth I] Focus chain H [auth J] Focus chain I [auth K] Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N] Focus chain M [auth O] Focus chain N [auth P] Focus chain O [auth Q] Focus chain P [auth R] Focus chain Q [auth S] Focus chain R [auth T] Focus chain S [auth U] Focus chain T [auth V] Interactions & Density Focus chain E [auth G] Focus chain F [auth H] Focus chain G [auth I] Focus chain H [auth J] Focus chain I [auth K] Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N] Focus chain M [auth O] Focus chain N [auth P] Focus chain O [auth Q] Focus chain P [auth R] Focus chain Q [auth S] Focus chain R [auth T] Focus chain S [auth U] Focus chain T [auth V]
Glycosylation Resources
GlyTouCan: G57229GY GlyCosmos: G57229GY

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth D] MOL2 format, chain V [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain V [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth D]	V [auth A], W [auth B], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain V [auth A] Focus chain W [auth B] Focus chain Y [auth D] Interactions & Density Focus chain V [auth A] Focus chain W [auth B] Focus chain Y [auth D]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain Z [auth D] Interactions & Density Focus chain Z [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900038 Query on PRD_900038	E [auth G] F [auth H] G [auth I] H [auth J] I [auth K] E [auth G], F [auth H], G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U], T [auth V]	lactulose	Oligosaccharide / Water retention		Interactions Focus chain E [auth G] Focus chain F [auth H] Focus chain G [auth I] Focus chain H [auth J] Focus chain I [auth K] Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N] Focus chain M [auth O] Focus chain N [auth P] Focus chain O [auth Q] Focus chain P [auth R] Focus chain Q [auth S] Focus chain R [auth T] Focus chain S [auth U] Focus chain T [auth V] Interactions & Density Focus chain E [auth G] Focus chain F [auth H] Focus chain G [auth I] Focus chain H [auth J] Focus chain I [auth K] Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N] Focus chain M [auth O] Focus chain N [auth P] Focus chain O [auth Q] Focus chain P [auth R] Focus chain Q [auth S] Focus chain R [auth T] Focus chain S [auth U] Focus chain T [auth V]