MolNFT v1 · #138323 · protein
Crystal structure of the tara wall teichoic acid glycosyltransferase bound to udp
5WFG · N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D…: “Crystal structure of the tara wall teichoic acid glycosyltransferase bound to udp”. X-ray diffraction, 1 ligand (UDP), 7 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5WFG
- Type
- protein
- Length
- 1,154 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase
- EC
- 2.4.1.187
- UniProt
- D3T4E0
- Ligands
- UDP
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 192 | 45% helix, 17% strand | D3T4E0 |
| B | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 193 | 44% helix, 18% strand | D3T4E0 |
| C | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 192 | 45% helix, 17% strand | D3T4E0 |
| E | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 194 | 46% helix, 18% strand | D3T4E0 |
| F | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 191 | 41% helix, 17% strand | D3T4E0 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 6 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.80 | 0.83 | 98 | empty |
| 2 | 1121 | 0.73 | 0.76 | 130 | UDP |
| 3 | 602 | 0.67 | 0.77 | 94 | UDP |
| 4 | 186 | 0.59 | 0.82 | 37 | empty |
| 5 | 309 | 0.58 | 0.77 | 59 | UDP |
Interfaces
10 interfaces between chains.
- B–C · 549 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 522 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 495 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 439 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 5WFG · Crystal structure of the TarA wall teichoic acid glycosyltransferase bound to UDP · 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 D3T4E0
- Elsewhere: RCSB PDB 5WFG · PDBe 5WFG · UniProt D3T4E0
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