MolNFT v1 · #143937 · protein
Crystal structure of vacv D13 in complex with rifampicin
6BED · Scaffold protein D13: “Crystal structure of vacv D13 in complex with rifampicin”. X-ray diffraction, 1 ligand (RFP), 20 pockets (best druggability 0.83). MolNFT v1 #143937 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6BED
- Type
- protein
- Length
- 1,615 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffold protein D13
- UniProt
- P68440
- Ligands
- RFP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scaffold protein D13 | protein | 542 | 17% helix, 40% strand | P68440 |
| B | Scaffold protein D13 | protein | 543 | 16% helix, 40% strand | P68440 |
| C | Scaffold protein D13 | protein | 530 | 15% helix, 41% strand | P68440 |
Ligands and binding sites
- RFP · Rifampicin · ligand · chains A, B, C
- FMT · Formic acid · additive · 15 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 10 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 | 1023 | 0.83 | 0.84 | 94 | empty |
| 2 | 1001 | 0.83 | 0.84 | 103 | FMT, EDO |
| 3 | 955 | 0.83 | 0.85 | 107 | FMT |
| 4 | 456 | 0.63 | 0.77 | 53 | empty |
| 5 | 120 | 0.53 | 0.82 | 25 | FMT, EDO |
Interfaces
3 interfaces between chains.
- A–B · 3000 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2763 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2461 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6BED · Crystal structure of VACV D13 in complex with Rifampicin · 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 6BED · PDBe 6BED · UniProt P68440
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