MolNFT v1 · #53403 · protein
EST1E from butyrivibrio proteoclasticus
2WTM: “EST1E from butyrivibrio proteoclasticus”. X-ray diffraction, 1 ligand (PO4), 13 pockets (best druggability 0.68). MolNFT v1 #53403 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WTM
- Type
- protein
- Length
- 985 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EST1E
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EST1E | protein | 250 | 35% helix, 27% strand | — |
| B | EST1E | protein | 242 | 37% helix, 27% strand | — |
| C | EST1E | protein | 250 | 35% helix, 27% strand | — |
| D | EST1E | protein | 243 | 36% helix, 27% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.68 | 0.90 | 22 | empty |
| 2 | 116 | 0.66 | 0.89 | 22 | empty |
| 3 | 242 | 0.55 | 0.78 | 35 | GOL |
| 4 | 196 | 0.54 | 0.78 | 30 | PO4 |
| 5 | 55 | 0.52 | 0.87 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1356 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1341 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 320 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WTM · Est1E from Butyrivibrio proteoclasticus · 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 2WTM · PDBe 2WTM
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