Research workbench
Structure of an ancestral glycosidase (family 1) bound to heme
Analyse Structure of an ancestral glycosidase (family 1) bound to heme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z1M
- Type
- protein
- Length
- 1,259 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancestral reconstructed glycosidase
- Ligands
- HEM, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancestral reconstructed glycosidase | protein | 423 | 46% helix, 15% strand | — |
| B | Ancestral reconstructed glycosidase | protein | 422 | 45% helix, 15% strand | — |
| C | Ancestral reconstructed glycosidase | protein | 414 | 47% helix, 16% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.82 | 0.83 | 95 | GOL |
| 2 | 385 | 0.78 | 0.87 | 35 | HEM |
| 3 | 440 | 0.78 | 0.86 | 46 | HEM, EDO |
| 4 | 529 | 0.77 | 0.84 | 47 | HEM |
| 5 | 618 | 0.72 | 0.79 | 54 | GOL, EDO |
Interfaces
3 interfaces between chains.
- B–C · 817 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 203 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Z1M · Structure of an Ancestral glycosidase (family 1) bound to heme · 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 6Z1M · PDBe 6Z1M
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