Research workbench
Crystal structure of dltd
Analyse Crystal structure of dltd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DXM
- Type
- protein
- Length
- 1,564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein dltd
- UniProt
- Q5M4V2
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein dltd | protein | 391 | 53% helix, 7% strand | Q5M4V2 |
| B, D | Protein dltd | protein | 392 | 54% helix, 7% strand | Q5M4V2 |
| C | Protein dltd | protein | 389 | 52% helix, 7% strand | Q5M4V2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.84 | 0.85 | 70 | empty |
| 2 | 1014 | 0.83 | 0.84 | 110 | SO4 |
| 3 | 667 | 0.74 | 0.81 | 51 | empty |
| 4 | 298 | 0.63 | 0.79 | 37 | empty |
| 5 | 62 | 0.63 | 0.93 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1341 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 851 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 323 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 180 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7DXM · Crystal structure of DltD · 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 Q5M4V2
- Elsewhere: RCSB PDB 7DXM · PDBe 7DXM · UniProt Q5M4V2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.