MolNFT v1 · #69320 · protein
Crystal structure of CBM42A from clostridium thermocellum
3KMV · Alpha-L-arabinofuranosidase B: “Crystal structure of CBM42A from clostridium thermocellum”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.55). MolNFT v1 #69320 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KMV
- Type
- protein
- Length
- 1,103 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-arabinofuranosidase B
- UniProt
- A3DBC8
- Ligands
- CA
- Pockets
- 10 · best druggability 0.55
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-arabinofuranosidase B | protein | 136 | 11% helix, 47% strand | A3DBC8 |
| B, G | Alpha-L-arabinofuranosidase B | protein | 138 | 12% helix, 48% strand | A3DBC8 |
| C, F | Alpha-L-arabinofuranosidase B | protein | 137 | 12% helix, 49% strand | A3DBC8 |
| D | Alpha-L-arabinofuranosidase B | protein | 138 | 11% helix, 48% strand | A3DBC8 |
| E | Alpha-L-arabinofuranosidase B | protein | 140 | 11% helix, 48% strand | A3DBC8 |
| H | Alpha-L-arabinofuranosidase B | protein | 139 | 11% helix, 47% strand | A3DBC8 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- FMT · Formic acid · additive · 19 copies · chains A, B, F, C, E, G, H
- GOL · Glycerol · additive · 6 copies · chains A, C, D, E, F, H
- ACT · Acetate ion · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.55 | 0.77 | 31 | FMT |
| 2 | 234 | 0.51 | 0.75 | 31 | empty |
| 3 | 80 | 0.48 | 0.83 | 25 | empty |
| 4 | 52 | 0.40 | 0.82 | 17 | empty |
| 5 | 112 | 0.39 | 0.75 | 25 | empty |
Interfaces
9 interfaces between chains.
- F–G · 676 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 664 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 383 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 374 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 373 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3KMV · Crystal structure of CBM42A from Clostridium thermocellum · 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 A3DBC8
- Elsewhere: RCSB PDB 3KMV · PDBe 3KMV · UniProt A3DBC8
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