Research workbench
Structure of the wall teichoic acid polymerase tagf, H444N + cdpg (15 minute soak)
Analyse Structure of the wall teichoic acid polymerase tagf, H444N + cdpg (15 minute… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L7K
- Type
- protein
- Length
- 1,625 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Teichoic acid biosynthesis protein F
- UniProt
- Q5HLM5
- Ligands
- EDT, C2G, CL, SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Teichoic acid biosynthesis protein F | protein | 410 | 42% helix, 15% strand | Q5HLM5 |
| B | Teichoic acid biosynthesis protein F | protein | 409 | 41% helix, 14% strand | Q5HLM5 |
| C | Teichoic acid biosynthesis protein F | protein | 411 | 41% helix, 15% strand | Q5HLM5 |
| D | Teichoic acid biosynthesis protein F | protein | 395 | 42% helix, 14% strand | Q5HLM5 |
Ligands and binding sites
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · 2 copies · chains A, B, C, D
- C2G · [cytidine-5'-phosphate] glycerylphosphoric acid ester · ligand · chains D
- CL · Chloride ion · ion · 22 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.75 | 0.81 | 60 | C2G, EDO |
| 2 | 631 | 0.68 | 0.77 | 58 | empty |
| 3 | 667 | 0.68 | 0.76 | 54 | SO4, CL |
| 4 | 609 | 0.67 | 0.77 | 43 | SO4, CL |
| 5 | 119 | 0.66 | 0.89 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 539 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 484 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 469 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 359 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 344 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3L7K · Structure of the Wall Teichoic Acid Polymerase TagF, H444N + CDPG (15 minute soak) · the same entry in another collection · chain D against D, TM-score 1.00
- Q5HLM5 · AlphaFold monomer V2.0 prediction for teichoic acid POLY(GLYCEROL phosphate) polymerase… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q5HLM5
- Elsewhere: RCSB PDB 3L7K · PDBe 3L7K · UniProt Q5HLM5
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