MolNFT v1 · #54972 · protein
B-repeat of listeria monocytogenes inlb (internalin B)
2Y5P: “B-repeat of listeria monocytogenes inlb (internalin B)”. X-ray diffraction, 2 ligands (CA, CL), 4 pockets (best druggability 0.53). MolNFT v1 #54972 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Y5P
- Type
- protein
- Length
- 289 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Internalin B
- UniProt
- P25147
- Ligands
- CA, CL
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Internalin B | protein | 72 | 0% helix, 49% strand | P25147 |
| C | Internalin B | protein | 73 | 0% helix, 51% strand | P25147 |
| D | Internalin B | protein | 72 | 0% helix, 54% strand | P25147 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.53 | 0.81 | 27 | CA |
| 2 | 70 | 0.34 | 0.76 | 17 | empty |
| 3 | 56 | 0.33 | 0.77 | 13 | empty |
| 4 | 51 | 0.27 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 651 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 590 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 511 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2Y5P · B-repeat of Listeria monocytogenes InlB (internalin B) · 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 P25147
- Elsewhere: RCSB PDB 2Y5P · PDBe 2Y5P · UniProt P25147
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.