MolNFT v1 · #137468 · protein
The crystal structure of a thioesteras from actinomadura verrucosospora.
5VPJ · Thioesterase: “The crystal structure of a thioesteras from actinomadura verrucosospora.”. X-ray diffraction, 1 ligand (CL), 18 pockets (best druggability 0.85). MolNFT v1 #137468 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5VPJ
- Type
- protein
- Length
- 1,638 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioesterase
- Ligands
- CL
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 12 distinct chains · 26% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioesterase | protein | 138 | 28% helix, 43% strand | — |
| B | Thioesterase | protein | 138 | 25% helix, 43% strand | — |
| C | Thioesterase | protein | 139 | 25% helix, 46% strand | — |
| D | Thioesterase | protein | 138 | 26% helix, 42% strand | — |
| E | Thioesterase | protein | 135 | 27% helix, 44% strand | — |
| F | Thioesterase | protein | 139 | 25% helix, 43% strand | — |
| G | Thioesterase | protein | 136 | 26% helix, 44% strand | — |
| H | Thioesterase | protein | 136 | 26% helix, 42% strand | — |
| I | Thioesterase | protein | 136 | 26% helix, 43% strand | — |
| J | Thioesterase | protein | 133 | 26% helix, 42% strand | — |
| K | Thioesterase | protein | 131 | 27% helix, 42% strand | — |
| L | Thioesterase | protein | 139 | 27% helix, 45% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B, G, H, K, L
- PG4 · Tetraethylene glycol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.85 | 0.86 | 71 | empty |
| 2 | 1064 | 0.85 | 0.86 | 77 | empty |
| 3 | 1035 | 0.84 | 0.86 | 67 | empty |
| 4 | 951 | 0.77 | 0.79 | 90 | CL |
| 5 | 217 | 0.76 | 0.90 | 43 | PG4 |
Interfaces
25 interfaces between chains.
- C–D · 915 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 842 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 826 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 822 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 5VPJ · The crystal structure of a thioesterase from Actinomadura verrucosospora · 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 5VPJ · PDBe 5VPJ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.