MolNFT v1 · #157480 · protein
Crystal structure of a glucose-1-phosphate thymidylyltransferase from burkholderia phymatum bound to 2'-deoxy-thymidine-B-L-rhamnose
6N0U: “Crystal structure of a glucose-1-phosphate thymidylyltransferase from burkholderia phymatum bound to…”. X-ray diffraction, 1 ligand (TRH), 19 pockets (best druggability 0.73). MolNFT v1 #157480 on GenesisL1: 3D structure, binding…
- PDB
- 6N0U
- Type
- protein
- Length
- 1,171 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphate thymidylyltransferase
- EC
- 2.7.7.24
- UniProt
- B2JFC5
- Ligands
- TRH
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 295 | 37% helix, 22% strand | B2JFC5 |
| B | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 293 | 37% helix, 22% strand | B2JFC5 |
| C | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 295 | 37% helix, 22% strand | B2JFC5 |
| D | Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) | protein | 288 | 38% helix, 23% strand | B2JFC5 |
Ligands and binding sites
- TRH · 2'-deoxy-thymidine-beta-L-rhamnose · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.98 | 14 | empty |
| 2 | 393 | 0.73 | 0.83 | 35 | empty |
| 3 | 378 | 0.72 | 0.83 | 36 | EDO |
| 4 | 456 | 0.71 | 0.82 | 41 | TRH |
| 5 | 468 | 0.70 | 0.81 | 49 | TRH |
Interfaces
3 interfaces between chains.
- A–B · 1878 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 1446 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 254 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6N0U · Crystal structure of a glucose-1-phosphate thymidylyltransferase from Burkholderia… · 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
- Every structure of UniProt B2JFC5
- Elsewhere: RCSB PDB 6N0U · PDBe 6N0U · UniProt B2JFC5
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