MolNFT v1 · #185429 · protein
Listeria monocytogene inlb (internalin B) residues 36-392 (internalin domain and B-repeat)
7PV9: “Listeria monocytogene inlb (internalin B) residues 36-392 (internalin domain and B-repeat)”. X-ray diffraction, 6 pockets (best druggability 0.59). MolNFT v1 #185429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7PV9
- Type
- protein
- Length
- 1,049 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Internalin B
- UniProt
- P0DQD2
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Internalin B | protein | 356 | 13% helix, 33% strand | P0DQD2 |
| C | Internalin B | protein | 337 | 13% helix, 30% strand | P0DQD2 |
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.59 | 0.77 | 29 | empty |
| 2 | 356 | 0.59 | 0.76 | 30 | empty |
| 3 | 309 | 0.59 | 0.78 | 36 | empty |
| 4 | 377 | 0.56 | 0.75 | 42 | empty |
| 5 | 197 | 0.55 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 715 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 626 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 359 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7PV9 · Listeria monocytogene InlB (internalin B) residues 36-392 (internalin domain and B-repeat) · the same entry in another collection · chain A against A, TM-score 1.00
- P0DQD2 · AlphaFold monomer V2.0 prediction for internalin B (P0DQD2) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0DQD2
- Elsewhere: RCSB PDB 7PV9 · PDBe 7PV9 · UniProt P0DQD2
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