Research workbench
Desgla-XAS195A bound to aptamer 11F7T
Analyse Desgla-XAS195A bound to aptamer 11F7T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VOE
- Type
- protein + DNA
- Length
- 318 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X; Aptamer 11F7T (36-mer)
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- MG, NA, CA
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Coagulation factor X (EC 3.4.21.6) | protein | 231 | 14% helix, 38% strand | P00742 |
| L | Coagulation factor X (EC 3.4.21.6) | protein | 51 | 8% helix, 27% strand | P00742 |
| A | Aptamer 11F7T (36-mer) | dna | 36 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains H
- CA · Calcium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.49 | 0.78 | 20 | empty |
| 2 | 101 | 0.45 | 0.80 | 22 | empty |
| 3 | 106 | 0.45 | 0.79 | 24 | empty |
| 4 | 103 | 0.43 | 0.77 | 25 | empty |
| 5 | 140 | 0.38 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- H–L · 874 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 744 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 19 modified, 8 disulfide (nucleotide modification, disulfide).
Compared structures
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 P00742
- Elsewhere: RCSB PDB 5VOE · PDBe 5VOE · UniProt P00742
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