Research workbench
Crystal structure of the tara wall teichoic acid glycosyltransferase bound to udp
Analyse Crystal structure of the tara wall teichoic acid glycosyltransferase bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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