8OL4

Structure of the C-terminal domains of the Bdellovibrio bacteriovorus Bd2439 fibre in complex with GlcNAc

PDB DOI: https://doi.org/10.2210/pdb8OL4/pdb

Classification: CELL ADHESION
Organism(s): Bdellovibrio bacteriovorus HD100
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-30 Released: 2023-10-25
Deposition Author(s): Caulton, S.G., Lovering, A.L.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.198
R-Value Work: 0.166
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Title to be confirmed

Caulton, S.G., Lovering, A.L.

To be published.

Macromolecule Content

Total Structure Weight: 93.05 kDa
Atom Count: 6,580
Modelled Residue Count: 768
Deposited Residue Count: 858
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell wall surface anchor family protein	A, B, C	286	Bdellovibrio bacteriovorus HD100	Mutation(s): 0 Gene Names: Bd2439
UniProt
Find proteins for Q6MKF5 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MKF5 Go to UniProtKB: Q6MKF5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6MKF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C]	G [auth A], L [auth B], P [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C]	D [auth A], I [auth B], N [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C]	F [auth A], J [auth B], K [auth B], O [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]