MolNFT v1 · #179107 · protein
Crystal structure of a GH43_12 retrieved from capybara gut metagenome
7JVH · Glycoside hydrolase family 43_12: “Crystal structure of a GH43_12 retrieved from capybara gut metagenome”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #179107 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7JVH
- Type
- protein
- Length
- 3,136 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 43_12
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase family 43_12 | protein | 535 | 4% helix, 44% strand | — |
| B | Glycoside hydrolase family 43_12 | protein | 535 | 4% helix, 44% strand | — |
| C | Glycoside hydrolase family 43_12 | protein | 536 | 4% helix, 44% strand | — |
| D | Glycoside hydrolase family 43_12 | protein | 534 | 3% helix, 44% strand | — |
| E | Glycoside hydrolase family 43_12 | protein | 497 | 3% helix, 40% strand | — |
| F | Glycoside hydrolase family 43_12 | protein | 499 | 4% helix, 40% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.76 | 0.78 | 84 | empty |
| 2 | 897 | 0.73 | 0.77 | 111 | GOL |
| 3 | 408 | 0.72 | 0.82 | 28 | empty |
| 4 | 404 | 0.72 | 0.83 | 28 | empty |
| 5 | 370 | 0.71 | 0.83 | 28 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1043 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 548 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 340 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 147 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 129 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 7JVH · Crystal structure of a GH43_12 retrieved from capybara gut metagenome · 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 7JVH · PDBe 7JVH
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