Research workbench
Crystal structure of cutibacterium acnes exo-beta-1,4-mannosidase
Analyse Crystal structure of cutibacterium acnes exo-beta-1,4-mannosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GVB
- Type
- protein
- Length
- 1,575 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-beta-1,4-mannosidase
- UniProt
- A0A2B7I7A6
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-beta-1,4-mannosidase | protein | 395 | 42% helix, 16% strand | A0A2B7I7A6 |
| B | Exo-beta-1,4-mannosidase | protein | 392 | 43% helix, 15% strand | A0A2B7I7A6 |
| C, D | Exo-beta-1,4-mannosidase | protein | 394 | 42% helix, 16% strand | A0A2B7I7A6 |
Ligands and binding sites
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.80 | 0.98 | 27 | empty |
| 2 | 113 | 0.80 | 0.98 | 27 | empty |
| 3 | 306 | 0.66 | 0.81 | 33 | MPO |
| 4 | 273 | 0.66 | 0.82 | 33 | MPO |
| 5 | 275 | 0.65 | 0.82 | 33 | MPO |
Interfaces
4 interfaces between chains.
- A–B · 1677 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1664 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 107 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GVB · Crystal structure of Cutibacterium acnes exo-beta-1,4-mannosidase · 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 A0A2B7I7A6
- Elsewhere: RCSB PDB 6GVB · PDBe 6GVB · UniProt A0A2B7I7A6
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