MolNFT v1 · #171337 · protein
Ancestral glycosidase (family 1)
6Z1H · Ancestral reconstructed glycosidase: “Ancestral glycosidase (family 1)”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.76). MolNFT v1 #171337 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z1H
- Type
- protein
- Length
- 786 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancestral reconstructed glycosidase; Residues 249 to 266 of chain a and 246 to 258 of…
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancestral reconstructed glycosidase | protein | 382 | 42% helix, 17% strand | — |
| B | Ancestral reconstructed glycosidase | protein | 373 | 45% helix, 18% strand | — |
| C | Residues 249 to 266 of chain a and 246 to 258 of chain B could not be identified and has been included as unk in chain C and D, respectively. | protein | 18 | 0% helix, 0% strand | — |
| D | Residues 249 to 266 of chain a and 246 to 258 of chain B could not be identified and has been included as unk in chain C and D, respectively. | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.76 | 0.91 | 25 | GOL, SO4 |
| 2 | 531 | 0.73 | 0.81 | 61 | empty |
| 3 | 305 | 0.73 | 0.85 | 39 | GOL |
| 4 | 94 | 0.58 | 0.87 | 21 | empty |
| 5 | 82 | 0.57 | 0.87 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 792 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 286 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Z1H · Ancestral glycosidase (family 1) · 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
- Elsewhere: RCSB PDB 6Z1H · PDBe 6Z1H
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