Research workbench
Crystal structure of vacv D13 in complex with 3-formyl rifamycin sv
Analyse Crystal structure of vacv D13 in complex with 3-formyl rifamycin sv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BEF
- Type
- protein
- Length
- 1,612 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffold protein D13
- UniProt
- P68440
- Ligands
- 3YI
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scaffold protein D13 | protein | 540 | 16% helix, 40% strand | P68440 |
| B | Scaffold protein D13 | protein | 543 | 16% helix, 40% strand | P68440 |
| C | Scaffold protein D13 | protein | 529 | 15% helix, 41% strand | P68440 |
Ligands and binding sites
- 3YI · (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16, 18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate · ligand · chains A, B, C
- FMT · Formic acid · additive · 8 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.84 | 0.84 | 106 | FMT |
| 2 | 919 | 0.83 | 0.85 | 102 | FMT |
| 3 | 1013 | 0.83 | 0.84 | 96 | empty |
| 4 | 430 | 0.63 | 0.78 | 44 | empty |
| 5 | 104 | 0.49 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2947 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2735 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2532 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 6BEF · Crystal structure of VACV D13 in complex with 3-formyl rifamycin SV · 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 P68440
- Elsewhere: RCSB PDB 6BEF · PDBe 6BEF · UniProt P68440
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