MolNFT v1 · #59063 · protein
Crystal structure of D-alanyl-lipoteichoic acid synthetase from streptococcus pneumoniae R6
3BMA: “Crystal structure of D-alanyl-lipoteichoic acid synthetase from streptococcus pneumoniae R6”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.85). MolNFT v1 #59063 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3BMA
- Type
- protein
- Length
- 2,345 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-lipoteichoic acid synthetase
- UniProt
- Q8DN13
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanyl-lipoteichoic acid synthetase | protein | 392 | 49% helix, 7% strand | Q8DN13 |
| B | D-alanyl-lipoteichoic acid synthetase | protein | 393 | 51% helix, 7% strand | Q8DN13 |
| C | D-alanyl-lipoteichoic acid synthetase | protein | 394 | 50% helix, 7% strand | Q8DN13 |
| D | D-alanyl-lipoteichoic acid synthetase | protein | 389 | 51% helix, 7% strand | Q8DN13 |
| E | D-alanyl-lipoteichoic acid synthetase | protein | 390 | 50% helix, 7% strand | Q8DN13 |
| F | D-alanyl-lipoteichoic acid synthetase | protein | 387 | 50% helix, 7% strand | Q8DN13 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, D, B, E, F
- GOL · Glycerol · additive · 10 copies · chains A, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.85 | 0.95 | 39 | GOL |
| 2 | 1088 | 0.82 | 0.83 | 95 | GOL |
| 3 | 795 | 0.81 | 0.84 | 67 | SO4 |
| 4 | 576 | 0.78 | 0.85 | 49 | empty |
| 5 | 333 | 0.69 | 0.83 | 36 | GOL, SO4 |
Interfaces
9 interfaces between chains.
- A–B · 1127 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 886 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 664 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 302 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 292 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3BMA · Crystal structure of D-alanyl-lipoteichoic acid synthetase from Streptococcus pneumoniae… · 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 Q8DN13
- Elsewhere: RCSB PDB 3BMA · PDBe 3BMA · UniProt Q8DN13
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