Research workbench
Structure of the wall teichoic acid polymerase tagf, H548A
Analyse Structure of the wall teichoic acid polymerase tagf, H548A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L7M
- Type
- protein
- Length
- 1,641 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, CL, PO4
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Teichoic acid biosynthesis protein F | protein | 407 | 42% helix, 14% strand | Q5HLM5 |
| B, C | Teichoic acid biosynthesis protein F | protein | 411 | 41% helix, 13% strand | Q5HLM5 |
| D | Teichoic acid biosynthesis protein F | protein | 412 | 42% helix, 15% strand | Q5HLM5 |
Ligands and binding sites
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 18 copies · chains A, B, D, C
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.66 | 0.76 | 43 | PO4, CL |
| 2 | 523 | 0.66 | 0.77 | 44 | PO4, CL |
| 3 | 538 | 0.65 | 0.76 | 52 | PO4 |
| 4 | 514 | 0.65 | 0.77 | 43 | PO4, CL |
| 5 | 120 | 0.65 | 0.88 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 555 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 486 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 478 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 344 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3L7M · Structure of the Wall Teichoic Acid Polymerase TagF, H548A · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.95
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 3L7M · PDBe 3L7M · UniProt Q5HLM5
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