MolNFT v1 · #143488 · protein
Crystal structure of cbmbc (family CBM26) from eubacterium rectale AMY13K
6B15: “Crystal structure of cbmbc (family CBM26) from eubacterium rectale AMY13K”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1 #143488 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6B15
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMY13K
- UniProt
- D6DYI9
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | AMY13K | protein | 209 | 0% helix, 43% strand | D6DYI9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 564 | 0.65 | 0.76 | 55 | empty |
| 2 | 425 | 0.63 | 0.77 | 57 | empty |
| 3 | 394 | 0.62 | 0.77 | 55 | EDO |
| 4 | 382 | 0.61 | 0.77 | 56 | empty |
| 5 | 311 | 0.60 | 0.78 | 44 | empty |
Interfaces
4 interfaces between chains.
- B–D · 503 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 501 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6B15 · Crystal structure of CBMbc (family CBM26) from Eubacterium rectale Amy13K · 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 D6DYI9
- Elsewhere: RCSB PDB 6B15 · PDBe 6B15 · UniProt D6DYI9
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