8VCQ

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

PDB DOI: https://doi.org/10.2210/pdb8VCQ/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: 2.09 Å
R-Value Free:
0.236 (Depositor), 0.227 (DCC)
R-Value Work:
0.202 (Depositor), 0.207 (DCC)
R-Value Observed:
0.217 (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: 152.34 kDa
Atom Count: 10,897
Modelled Residue Count: 1,200
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
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose	AA [auth c], BA [auth d], CA [auth e], DA [auth f], EA [auth g], AA [auth c], BA [auth d], CA [auth e], DA [auth f], EA [auth g], FA [auth h], GA [auth i], HA [auth j], I, 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], U [auth W], V [auth X], W [auth Y], X [auth Z], Y [auth a], Z [auth b]	3		N/A	Interactions Focus chain AA [auth c] Focus chain BA [auth d] Focus chain CA [auth e] Focus chain DA [auth f] Focus chain EA [auth g] Focus chain FA [auth h] Focus chain GA [auth i] Focus chain HA [auth j] Focus chain I 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] Focus chain U [auth W] Focus chain V [auth X] Focus chain W [auth Y] Focus chain X [auth Z] Focus chain Y [auth a] Focus chain Z [auth b] Interactions & Density Focus chain AA [auth c] Focus chain BA [auth d] Focus chain CA [auth e] Focus chain DA [auth f] Focus chain EA [auth g] Focus chain FA [auth h] Focus chain GA [auth i] Focus chain HA [auth j] Focus chain I 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] Focus chain U [auth W] Focus chain V [auth X] Focus chain W [auth Y] Focus chain X [auth Z] Focus chain Y [auth a] Focus chain Z [auth b]
Glycosylation Resources
GlyTouCan: G40178VU GlyCosmos: G40178VU

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain MA [auth F] MOL2 format, chain JA [auth D] MOL2 format, chain MA [auth F] mmCIF format, chain JA [auth D] mmCIF format, chain MA [auth F]	JA [auth D], MA [auth F]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Focus chain MA [auth F] Interactions & Density Focus chain JA [auth D] Focus chain MA [auth F]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain KA [auth D] SDF format, chain OA [auth F] MOL2 format, chain KA [auth D] MOL2 format, chain OA [auth F] mmCIF format, chain KA [auth D] mmCIF format, chain OA [auth F]	KA [auth D], OA [auth F]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain KA [auth D] Focus chain OA [auth F] Interactions & Density Focus chain KA [auth D] Focus chain OA [auth F]
GLA (Subject of Investigation/LOI) Query on GLA Download Ideal Coordinates CCD File SDF format, chain IA [auth A] SDF format, chain QA [auth G] MOL2 format, chain IA [auth A] MOL2 format, chain QA [auth G] mmCIF format, chain IA [auth A] mmCIF format, chain QA [auth G]	IA [auth A], QA [auth G]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain IA [auth A] Focus chain QA [auth G] Interactions & Density Focus chain IA [auth A] Focus chain QA [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain PA [auth F] MOL2 format, chain PA [auth F] mmCIF format, chain PA [auth F]	PA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain PA [auth F] Interactions & Density Focus chain PA [auth F]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain NA [auth F] MOL2 format, chain NA [auth F] mmCIF format, chain NA [auth F]	NA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain NA [auth F] Interactions & Density Focus chain NA [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain LA [auth D] MOL2 format, chain LA [auth D] mmCIF format, chain LA [auth D]	LA [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain LA [auth D] Interactions & Density Focus chain LA [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900002 Query on PRD_900002	AA [auth I] BA [auth L] CA [auth M] DA [auth N] EA [auth O] AA [auth I], BA [auth L], CA [auth M], DA [auth N], EA [auth O], FA [auth P], GA [auth Q], HA [auth R], I [auth S], J [auth T], K [auth U], L [auth V], M [auth W], N [auth X], O [auth Y], P [auth Z], Q [auth a], R [auth b], S [auth c], T [auth d], U [auth e], V [auth f], W [auth g], X [auth h], Y [auth i], Z [auth j]	raffinose	Oligosaccharide / Nutrient		Interactions Focus chain AA [auth c] Focus chain BA [auth d] Focus chain CA [auth e] Focus chain DA [auth f] Focus chain EA [auth g] Focus chain FA [auth h] Focus chain GA [auth i] Focus chain HA [auth j] Focus chain I 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] Focus chain U [auth W] Focus chain V [auth X] Focus chain W [auth Y] Focus chain X [auth Z] Focus chain Y [auth a] Focus chain Z [auth b] Interactions & Density Focus chain AA [auth c] Focus chain BA [auth d] Focus chain CA [auth e] Focus chain DA [auth f] Focus chain EA [auth g] Focus chain FA [auth h] Focus chain GA [auth i] Focus chain HA [auth j] Focus chain I 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] Focus chain U [auth W] Focus chain V [auth X] Focus chain W [auth Y] Focus chain X [auth Z] Focus chain Y [auth a] Focus chain Z [auth b]