6Y0X

Fucosylated antimicrobial peptide SB6 in complex with the lectin LecRSL from Ralstonia solanacearum at 2.4 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6Y0X/pdb

Classification: ANTIBIOTIC
Organism(s): Ralstonia solanacearum, synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-02-10 Released: 2021-02-17
Deposition Author(s): Baeriswyl, S., Stocker, A., Reymond, J.-L.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.280
R-Value Work: 0.243
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Fucosylated antimicrobial peptide SB6 in complex with the lectin LecRSL from Ralstonia solanacearum at 2.4 Angstrom resolution

Baeriswyl, S., Stocker, A., Reymond, J.-L.

To be published.

Macromolecule Content

Total Structure Weight: 73.25 kDa
Atom Count: 4,927
Modelled Residue Count: 621
Deposited Residue Count: 647
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A B E [auth C] H [auth D] J [auth E] A, B, E [auth C], H [auth D], J [auth E], L [auth F]	91	Ralstonia solanacearum	Mutation(s): 0 Gene Names: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum) Explore A0A0S4TLR1 Go to UniProtKB: A0A0S4TLR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0S4TLR1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SB6	C [auth I], F [auth K], N [auth R]	12	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SB6	D [auth J], G [auth L], I [auth M], K [auth O], M [auth Q]	13	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZDC (Subject of Investigation/LOI) Query on ZDC Download Ideal Coordinates CCD File SDF format, chain AA [auth R] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth I] SDF format, chain S [auth J] SDF format, chain T [auth K] SDF format, chain U [auth L] SDF format, chain V [auth D] SDF format, chain W [auth M] SDF format, chain X [auth E] SDF format, chain Y [auth O] SDF format, chain Z [auth Q] MOL2 format, chain AA [auth R] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth I] MOL2 format, chain S [auth J] MOL2 format, chain T [auth K] MOL2 format, chain U [auth L] MOL2 format, chain V [auth D] MOL2 format, chain W [auth M] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth O] MOL2 format, chain Z [auth Q]	AA [auth R] O [auth A] Q [auth A] R [auth I] S [auth J] AA [auth R], O [auth A], Q [auth A], R [auth I], S [auth J], T [auth K], U [auth L], V [auth D], W [auth M], X [auth E], Y [auth O], Z [auth Q]	3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid C₈ H₁₄ O₆ YTZUDUWVQZSKNN-OASCRQMUSA-N		Interactions Focus chain AA [auth R] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth K] Focus chain U [auth L] Focus chain V [auth D] Focus chain W [auth M] Focus chain X [auth E] Focus chain Y [auth O] Focus chain Z [auth Q] Interactions & Density Focus chain AA [auth R] Focus chain O [auth A] Focus chain Q [auth A] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth K] Focus chain U [auth L] Focus chain V [auth D] Focus chain W [auth M] Focus chain X [auth E] Focus chain Y [auth O] Focus chain Z [auth Q]
DLY (Subject of Investigation/LOI) Query on DLY Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	D-LYSINE C₆ H₁₄ N₂ O₂ KDXKERNSBIXSRK-RXMQYKEDSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]