Research workbench
Crystal structure of an extracellular domain of arabinofuranosyltransferase from corynebacterium diphtheriae
Analyse Crystal structure of an extracellular domain of arabinofuranosyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BYW
- Type
- protein
- Length
- 1,269 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative arabinofuranosyltransferase
- UniProt
- Q6NK78
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative arabinofuranosyltransferase | protein | 157 | 15% helix, 42% strand | Q6NK78 |
| B, E, G | Putative arabinofuranosyltransferase | protein | 159 | 16% helix, 42% strand | Q6NK78 |
| C | Putative arabinofuranosyltransferase | protein | 160 | 13% helix, 42% strand | Q6NK78 |
| D | Putative arabinofuranosyltransferase | protein | 157 | 15% helix, 41% strand | Q6NK78 |
| F | Putative arabinofuranosyltransferase | protein | 160 | 14% helix, 43% strand | Q6NK78 |
| H | Putative arabinofuranosyltransferase | protein | 158 | 16% helix, 44% strand | Q6NK78 |
Ligands and binding sites
- ZN · Zinc ion · metal · 19 copies · chains A, B, C, D, E, F, G
- ACT · Acetate ion · additive · 13 copies · chains A, B, C, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.70 | 0.78 | 75 | empty |
| 2 | 556 | 0.64 | 0.76 | 57 | empty |
| 3 | 154 | 0.63 | 0.86 | 36 | empty |
| 4 | 572 | 0.63 | 0.75 | 48 | empty |
| 5 | 108 | 0.59 | 0.86 | 26 | empty |
Interfaces
13 interfaces between chains.
- E–F · 2456 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 2258 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2245 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2173 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 401 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3BYW · Crystal structure of an extracellular domain of arabinofuranosyltransferase from… · 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 Q6NK78
- Elsewhere: RCSB PDB 3BYW · PDBe 3BYW · UniProt Q6NK78
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