MolNFT v1 · #125609 · protein
Structure of yersinia pseudotuberculosis invd
5LDY · Ig domain protein group 1 domain protein: “Structure of yersinia pseudotuberculosis invd”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.63). MolNFT v1 #125609 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LDY
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig domain protein group 1 domain protein
- UniProt
- A0A0H3B1G5
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig domain protein group 1 domain protein | protein | 335 | 1% helix, 48% strand | A0A0H3B1G5 |
| B | Ig domain protein group 1 domain protein | protein | 339 | 3% helix, 49% strand | A0A0H3B1G5 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.63 | 0.81 | 31 | empty |
| 2 | 322 | 0.60 | 0.78 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 673 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5LDY · Structure of Yersinia pseudotuberculosis InvD · 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 A0A0H3B1G5
- Elsewhere: RCSB PDB 5LDY · PDBe 5LDY · UniProt A0A0H3B1G5
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