MolNFT v1 · #55025 · protein
Crystal structure of unliganded gtb P156L
2Y7A · Abo glycosyltransferase: “Crystal structure of unliganded gtb P156L”. X-ray diffraction, 2 ligands (UDP, MN), 13 pockets (best druggability 0.74). MolNFT v1 #55025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Y7A
- Type
- protein
- Length
- 1,102 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abo glycosyltransferase
- EC
- 2.4.1.37
- UniProt
- Q70V26
- Ligands
- UDP, MN
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abo glycosyltransferase (EC 2.4.1.37) | protein | 277 | 32% helix, 20% strand | Q70V26 |
| B | Abo glycosyltransferase (EC 2.4.1.37) | protein | 276 | 34% helix, 21% strand | Q70V26 |
| C | Abo glycosyltransferase (EC 2.4.1.37) | protein | 268 | 31% helix, 22% strand | Q70V26 |
| D | Abo glycosyltransferase (EC 2.4.1.37) | protein | 281 | 32% helix, 20% strand | Q70V26 |
Ligands and binding sites
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 | 725 | 0.74 | 0.80 | 47 | empty |
| 2 | 500 | 0.63 | 0.75 | 39 | empty |
| 3 | 347 | 0.59 | 0.76 | 33 | empty |
| 4 | 353 | 0.57 | 0.75 | 24 | empty |
| 5 | 265 | 0.54 | 0.76 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2489 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 204 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 198 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 192 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2Y7A · Crystal structure of unliganded GTB P156L · the same entry in another collection · chain D against D, 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 Q70V26
- Elsewhere: RCSB PDB 2Y7A · PDBe 2Y7A · UniProt Q70V26
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