MolNFT v1 · #138185 · protein
Crystal structure of the tara wall teichoic acid glycosyltransferase
5WB4 · N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D…: “Crystal structure of the tara wall teichoic acid glycosyltransferase”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.85). MolNFT v1 #138185 on…
- PDB
- 5WB4
- Type
- protein
- Length
- 1,547 residues
- Chains
- 8
- 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
- SO4
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 194 | 40% helix, 19% strand | D3T4E0 |
| B | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 194 | 42% helix, 19% strand | D3T4E0 |
| C, D, H | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 193 | 43% helix, 18% strand | D3T4E0 |
| E | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 191 | 43% helix, 18% strand | D3T4E0 |
| F | N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D- mannosaminyltransferase (EC 2.4.1.187) | protein | 195 | 41% helix, 18% strand | D3T4E0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, E, B, D, C, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.85 | 0.88 | 95 | SO4 |
| 2 | 427 | 0.82 | 0.90 | 49 | SO4 |
| 3 | 416 | 0.82 | 0.90 | 50 | SO4 |
| 4 | 818 | 0.82 | 0.84 | 95 | empty |
| 5 | 623 | 0.72 | 0.79 | 57 | empty |
Interfaces
18 interfaces between chains.
- C–F · 1169 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 1143 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 1122 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 394 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 393 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 modified (engineered).
Compared structures
- 5WB4 · Crystal structure of the TarA wall teichoic acid glycosyltransferase · 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 D3T4E0
- Elsewhere: RCSB PDB 5WB4 · PDBe 5WB4 · UniProt D3T4E0
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