MolNFT v1 · #161214 · protein
Structure of fucosylated D-antimicrobial peptide SB4 in complex with the fucose-binding lectin pa-iil at 2.009 ångström resolution
6Q79: “Structure of fucosylated D-antimicrobial peptide SB4 in complex with the fucose-binding lectin pa-iil at…”. X-ray diffraction, 3 ligands (ZDC, CA, NH2), 5 pockets (best druggability 0.37). MolNFT v1 #161214 on GenesisL1: 3D…
- PDB
- 6Q79
- Type
- protein
- Length
- 494 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin; SB4; SB4 incomplete
- UniProt
- A0A069Q9V4
- Ligands
- ZDC, CA, NH2
- Pockets
- 5 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin | protein | 114 | 0% helix, 71% strand | A0A069Q9V4 |
| E, H | SB4 | protein | 13 | 77% helix, 0% strand | — |
| F, G | SB4 incomplete | protein | 6 | 0% 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, D, B, F, C, G, H
- CA · Calcium ion · metal · 8 copies · chains A, D, B, C, G
- NH2 · Amino group · ion · 2 copies · chains E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.37 | 0.74 | 19 | empty |
| 2 | 72 | 0.36 | 0.77 | 19 | ZDC |
| 3 | 102 | 0.34 | 0.73 | 18 | empty |
| 4 | 70 | 0.34 | 0.76 | 22 | ZDC |
| 5 | 57 | 0.29 | 0.76 | 17 | ZDC |
Interfaces
12 interfaces between chains.
- A–D · 1339 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1323 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 516 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 220 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 d-amino, 4 glycan (D-amino acid, glycosylation).
Compared structures
- 6Q79 · Structure of Fucosylated D-antimicrobial peptide SB4 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 6Q79 · PDBe 6Q79 · UniProt A0A069Q9V4
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