Research workbench
Crystal structure of the glycosyltransferase babsha bound with udp and L-malate
Analyse Crystal structure of the glycosyltransferase babsha bound with udp and L-malate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MBO
- Type
- protein
- Length
- 2,961 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase, group 1 family
- UniProt
- Q81ST7
- Ligands
- UDP, MLT, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase, group 1 family | protein | 372 | 43% helix, 16% strand | Q81ST7 |
| B | Glycosyltransferase, group 1 family | protein | 369 | 41% helix, 15% strand | Q81ST7 |
| C | Glycosyltransferase, group 1 family | protein | 373 | 41% helix, 14% strand | Q81ST7 |
| D, H | Glycosyltransferase, group 1 family | protein | 369 | 43% helix, 16% strand | Q81ST7 |
| E | Glycosyltransferase, group 1 family | protein | 375 | 41% helix, 15% strand | Q81ST7 |
| F | Glycosyltransferase, group 1 family | protein | 369 | 41% helix, 13% strand | Q81ST7 |
| G | Glycosyltransferase, group 1 family | protein | 365 | 37% helix, 15% strand | Q81ST7 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, C, E, H
- MLT · D-malate · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 2 copies · chains C, E
- GOL · Glycerol · additive · 21 copies · chains A, B, C, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.83 | 0.85 | 63 | empty |
| 2 | 681 | 0.81 | 0.85 | 73 | GOL |
| 3 | 543 | 0.81 | 0.87 | 63 | UDP, GOL, MLT, MG |
| 4 | 721 | 0.80 | 0.84 | 67 | empty |
| 5 | 490 | 0.80 | 0.87 | 69 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1707 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1646 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1597 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1562 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 784 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 3MBO · Crystal Structure of the Glycosyltransferase BaBshA bound with UDP and L-malate · the same entry in another collection · chain G against G, TM-score 1.00
- Q81ST7 · AlphaFold monomer V2.0 prediction for N-acetyl-alpha-D-glucosaminyl L-malate synthase… · a predicted model of the same protein · chain H against A, TM-score 0.97
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 Q81ST7
- Elsewhere: RCSB PDB 3MBO · PDBe 3MBO · UniProt Q81ST7
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