8Q82 | pdb_00008q82

Photorhabdus laumondii lectin PLL4 in complex with alpha-methyl-fucoside

PDB DOI: https://doi.org/10.2210/pdb8Q82/pdb

Classification: CELL ADHESION
Organism(s): Photorhabdus laumondii subsp. laumondii TTO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-17 Released: 2025-03-05
Deposition Author(s): Melicher, F., Houser, J., Paulenova, E., Wimmerova, M.
Funding Organization(s): Grant Agency of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.240 (Depositor), 0.246 (DCC)
R-Value Work:
0.205 (Depositor), 0.212 (DCC)

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

The insight into the biology of five homologous lectins produced by the entomopathogenic bacterium and nematode symbiont Photorhabdus laumondii

Paulenova, E., Dobes, P., Melicher, F., Houser, J., Faltinek, L., Kodakov, N., Kononov, L., Hyrsl, P., Wimmerova, M.

To be published.

Macromolecule Content

Total Structure Weight: 81.74 kDa
Atom Count: 5,459
Modelled Residue Count: 672
Deposited Residue Count: 738
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17	A, B	369	Photorhabdus laumondii subsp. laumondii TTO1	Mutation(s): 0 Gene Names: plu0736
UniProt
Find proteins for Q7N8I6 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)) Explore Q7N8I6 Go to UniProtKB: Q7N8I6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7N8I6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MFU (Subject of Investigation/LOI) Query on MFU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	C [auth A], D [auth A], E [auth A], H [auth B]	methyl alpha-L-fucopyranoside C₇ H₁₄ O₅ OHWCAVRRXKJCRB-CXNFULCWSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]