MolNFT v1 · #53319 · protein
Internalin domain of listeria monocytogenes inlb: triclinic crystal form
2WQU · Internalin B: “Internalin domain of listeria monocytogenes inlb: triclinic crystal form”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.68). MolNFT v1 #53319 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2WQU
- Type
- protein
- Length
- 1,682 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Internalin B
- UniProt
- P25147
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Internalin B | protein | 285 | 15% helix, 27% strand | P25147 |
| B | Internalin B | protein | 280 | 18% helix, 26% strand | P25147 |
| C | Internalin B | protein | 264 | 19% helix, 22% strand | P25147 |
| D | Internalin B | protein | 285 | 15% helix, 27% strand | P25147 |
| E, F | Internalin B | protein | 284 | 18% helix, 27% strand | P25147 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, E, F
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.68 | 0.78 | 71 | empty |
| 2 | 234 | 0.61 | 0.81 | 25 | empty |
| 3 | 292 | 0.60 | 0.78 | 32 | SO4 |
| 4 | 333 | 0.60 | 0.77 | 32 | empty |
| 5 | 217 | 0.59 | 0.81 | 36 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1315 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 742 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 718 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 469 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 446 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2WQU · Internalin domain of Listeria monocytogenes InlB: triclinic crystal form · 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 2WQU · PDBe 2WQU · UniProt P25147
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