MolNFT v1 · #136228 · protein
Clostridium difficile tcda-crops bound to PA50 Fab
5UMI · Toxin a: “Clostridium difficile tcda-crops bound to PA50 Fab”. X-ray diffraction, 9 pockets (best druggability 0.58). MolNFT v1 #136228 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UMI
- Type
- protein
- Length
- 886 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin a; PA50 Fab light chain; PA50 Fab heavy chain
- EC
- 3.4.22.-
- UniProt
- P16154
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Toxin a (EC 3.4.22.-) | protein | 245 | 0% helix, 48% strand | P16154 |
| L | PA50 Fab light chain | protein | 210 | 3% helix, 47% strand | — |
| H | PA50 Fab heavy chain | protein | 213 | 6% helix, 50% strand | — |
| B | PA50 Fab light chain | protein | 101 | 3% helix, 42% strand | — |
| A | PA50 Fab heavy chain | protein | 117 | 0% helix, 38% strand | — |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.58 | 0.75 | 49 | empty |
| 2 | 128 | 0.41 | 0.75 | 20 | empty |
| 3 | 116 | 0.40 | 0.75 | 28 | empty |
| 4 | 114 | 0.39 | 0.75 | 20 | empty |
| 5 | 51 | 0.33 | 0.78 | 14 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1794 Ų buried · 18 hydrogen bonds · protein-protein
- C–H · 845 Ų buried · 10 hydrogen bonds · protein-protein
- C–A · 833 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 815 Ų buried · 8 hydrogen bonds · protein-protein
- C–L · 419 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5UMI · Clostridium difficile TcdA-CROPs bound to PA50 Fab · the same entry in another collection · chain C against C, 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 P16154
- Elsewhere: RCSB PDB 5UMI · PDBe 5UMI · UniProt P16154
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