Research workbench
Crystal structure of vacv D13 in complex with rifamycin sv
Analyse Crystal structure of vacv D13 in complex with rifamycin sv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BEB
- Type
- protein
- Length
- 1,600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffold protein D13
- UniProt
- P68440
- Ligands
- RFV
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scaffold protein D13 | protein | 531 | 15% helix, 41% strand | P68440 |
| B | Scaffold protein D13 | protein | 530 | 15% helix, 40% strand | P68440 |
| C | Scaffold protein D13 | protein | 539 | 15% helix, 40% strand | P68440 |
Ligands and binding sites
- RFV · rifamycin SV · ligand · chains A, B, C
- FMT · Formic acid · additive · 23 copies · chains A, B, C
- 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.84 | 0.85 | 111 | FMT |
| 2 | 1089 | 0.84 | 0.85 | 111 | empty |
| 3 | 748 | 0.78 | 0.82 | 81 | FMT |
| 4 | 792 | 0.78 | 0.81 | 70 | FMT |
| 5 | 467 | 0.62 | 0.76 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2627 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2563 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2363 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6BEB · Crystal structure of VACV D13 in complex with 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 6BEB · PDBe 6BEB · UniProt P68440
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