Research workbench
Crystal structure of vacv D13 in complex with rifaximin
Analyse Crystal structure of vacv D13 in complex with rifaximin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BEE
- Type
- protein
- Length
- 1,613 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffold protein D13
- UniProt
- P68440
- Ligands
- RXM
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scaffold protein D13 | protein | 542 | 16% helix, 40% strand | P68440 |
| B | Scaffold protein D13 | protein | 542 | 15% helix, 40% strand | P68440 |
| C | Scaffold protein D13 | protein | 529 | 15% helix, 41% strand | P68440 |
Ligands and binding sites
- RXM · (2S,16Z,18E,20S,21S,22R,23R,24R,25S,26R,27S,28E)-5,6, 21,23-tetrahydroxy-27-methoxy-2,4,11,16,20,22,24,26-octamethyl-1,15-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)furo[2'',3'':7', 8']naphtho[1',2':4,5]imidazo[1,2-a]pyridin-25-yl acetate · ligand · chains A, B, C
- FMT · Formic acid · additive · 5 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 4 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.83 | 0.85 | 92 | empty |
| 2 | 983 | 0.83 | 0.84 | 92 | FMT |
| 3 | 680 | 0.78 | 0.83 | 61 | FMT |
| 4 | 505 | 0.70 | 0.79 | 44 | empty |
| 5 | 385 | 0.61 | 0.77 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2984 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2786 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2509 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6BEE · Crystal structure of VACV D13 in complex with Rifaximin · 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 6BEE · PDBe 6BEE · UniProt P68440
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