MolNFT v1 · #161202 · protein

Structure of fucosylated D-antimicrobial peptide SB6 in complex with the fucose-binding lectin pa-iil at 1.525 ångström resolution

6Q6X: “Structure of fucosylated D-antimicrobial peptide SB6 in complex with the fucose-binding lectin pa-iil at…”. X-ray diffraction, 3 ligands (ZDC, CA, NH2), 6 pockets (best druggability 0.68). MolNFT v1 #161202 on GenesisL1: 3D…

PDB: 6Q6X
Type: protein
Length: 504 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fucose-binding lectin; SB6
UniProt: A0A069Q9V4
Ligands: ZDC, CA, NH2
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Fucose-binding lectin	protein	114	0% helix, 63% strand	A0A069Q9V4
E, F, G, H	SB6	protein	12	67% helix, 0% strand	—

Ligands and binding sites

ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 4 copies · chains A, E, C, B, F, D, G, H
CA · Calcium ion · metal · 8 copies · chains A, C, B, D
NH2 · Amino group · ion · 4 copies · chains E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	746	0.68	0.76	78	ZDC
2	196	0.50	0.77	35	empty
3	135	0.41	0.75	19	ZDC
4	88	0.38	0.77	20	ZDC
5	54	0.32	0.77	16	CA, ZDC

Interfaces

11 interfaces between chains.

A–C · 1329 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1325 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 412 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 160 Å² buried · 1 hydrogen bond · protein-protein
B–F · 128 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 d-amino, 4 glycan (D-amino acid, glycosylation).

Compared structures

6Q6X · Structure of Fucosylated D-antimicrobial peptide SB6 in complex with the Fucose-binding… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A069Q9V4
Elsewhere: RCSB PDB 6Q6X · PDBe 6Q6X · UniProt A0A069Q9V4

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