MolNFT v1 · #52334 · protein
Screening a limited structure-based library identifies udp-galnac- specific mutants of alpha-1,3 galactosyltransferase
2VXM · N-acetyllactosaminide alpha-1,3-galactosyltransferase: “Screening a limited structure-based library identifies udp-galnac- specific mutants of alpha-1,3…”. X-ray diffraction, 9 pockets (best druggability 0.68). MolNFT v1 #52334 on…
- PDB
- 2VXM
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyllactosaminide alpha-1,3-galactosyltransferase
- EC
- 2.4.1.87
- UniProt
- P14769
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) | protein | 268 | 34% helix, 22% strand | P14769 |
| B | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) | protein | 251 | 30% helix, 20% strand | P14769 |
| C | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) | protein | 254 | 33% helix, 20% strand | P14769 |
| D | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) | protein | 259 | 32% helix, 20% strand | P14769 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.68 | 0.75 | 66 | GOL |
| 2 | 768 | 0.68 | 0.75 | 85 | empty |
| 3 | 250 | 0.60 | 0.79 | 32 | empty |
| 4 | 227 | 0.57 | 0.79 | 33 | empty |
| 5 | 202 | 0.52 | 0.77 | 38 | empty |
Interfaces
2 interfaces between chains.
- C–D · 714 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 444 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VXM · Screening a Limited Structure-based Library Identifies UDP-GalNAc- Specific Mutants of… · the same entry in another collection · chain D against D, TM-score 1.00
- P14769 · AlphaFold monomer V2.0 prediction for N-acetyllactosaminide… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P14769
- Elsewhere: RCSB PDB 2VXM · PDBe 2VXM · UniProt P14769
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