MolNFT v1 · #75034 · protein
Structures of clostridium thermocellum cbha FIBRONECTIN(III)-like modules
3PE9: “Structures of clostridium thermocellum cbha FIBRONECTIN(III)-like modules”. X-ray diffraction, 1 ligand (IOD), 4 pockets (best druggability 0.78). MolNFT v1 #75034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3PE9
- Type
- protein
- Length
- 351 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FIBRONECTIN(III)-like module
- UniProt
- A3DCH2
- Ligands
- IOD
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | FIBRONECTIN(III)-like module | protein | 90 | 0% helix, 61% strand | A3DCH2 |
| B | FIBRONECTIN(III)-like module | protein | 86 | 0% helix, 64% strand | A3DCH2 |
| D | FIBRONECTIN(III)-like module | protein | 85 | 0% helix, 58% strand | A3DCH2 |
Ligands and binding sites
- IOD · Iodide ion · ion · 11 copies · chains A, B, 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 | 711 | 0.78 | 0.83 | 88 | empty |
| 2 | 66 | 0.46 | 0.83 | 16 | empty |
| 3 | 138 | 0.46 | 0.77 | 23 | empty |
| 4 | 142 | 0.44 | 0.75 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–D · 483 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 254 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 176 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PE9 · Structures of Clostridium thermocellum CbhA fibronectin(III)-like modules · 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 A3DCH2
- Elsewhere: RCSB PDB 3PE9 · PDBe 3PE9 · UniProt A3DCH2
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