Research workbench
Single-particle cryo-EM structure of arabinofuranosyltransferase aftd from mycobacteria
Analyse Single-particle cryo-EM structure of arabinofuranosyltransferase aftd from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W98
- Type
- protein
- Length
- 1,389 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F5/8 type C domain-containing protein; Acyl carrier protein
- UniProt
- A0A1N1NKH9, P0A6A8
- Ligands
- 6OU, PNS, CA
- Pockets
- 17 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F5/8 type C domain-containing protein | protein | 1312 | 32% helix, 24% strand | A0A1N1NKH9 |
| B | Acyl carrier protein | protein | 77 | 58% helix, 3% strand | P0A6A8 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · chains A
- PNS · 4'-phosphopantetheine · ligand · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.79 | 0.81 | 121 | empty |
| 2 | 150 | 0.78 | 0.95 | 31 | empty |
| 3 | 1046 | 0.73 | 0.77 | 90 | 6OU, PNS |
| 4 | 92 | 0.72 | 0.95 | 23 | empty |
| 5 | 64 | 0.69 | 0.96 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 354 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 cofactor (disulfide, phosphopantetheinylation).
Compared structures
- 6W98 · Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6A8 · AlphaFold monomer V2.0 prediction for acyl carrier protein (P0A6A8) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 A0A1N1NKH9
- Every structure of UniProt P0A6A8
- Elsewhere: RCSB PDB 6W98 · PDBe 6W98 · UniProt A0A1N1NKH9 · UniProt P0A6A8
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