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Structure of a glycosyltransferase from leptospira borgpetersenii serovar hardjo-bovis (strain JB197)
Analyse Structure of a glycosyltransferase from leptospira borgpetersenii serovar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P61
- Type
- protein
- Length
- 767 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase
- UniProt
- Q04TP4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glycosyltransferase | protein | 193 | 32% helix, 29% strand | Q04TP4 |
| B | Glycosyltransferase | protein | 191 | 31% helix, 29% strand | Q04TP4 |
| C | Glycosyltransferase | protein | 190 | 33% helix, 29% strand | Q04TP4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D
- CIT · Citric acid · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.79 | 0.94 | 26 | EDO, GOL |
| 2 | 165 | 0.79 | 0.94 | 26 | GOL |
| 3 | 367 | 0.59 | 0.77 | 38 | empty |
| 4 | 93 | 0.47 | 0.81 | 19 | CIT |
| 5 | 116 | 0.37 | 0.74 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–D · 671 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 598 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 412 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 170 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6P61 · Structure of a Glycosyltransferase from Leptospira borgpetersenii serovar Hardjo-bovis… · the same entry in another collection · chain C against C, 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 Q04TP4
- Elsewhere: RCSB PDB 6P61 · PDBe 6P61 · UniProt Q04TP4
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