MolNFT v1 · #70316 · protein
Structure of probable D-alanine-POLY(PHOSPHORIBITOL) ligase subunit-1 from streptococcus pyogenes with ATP
3LGX · D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1: “Structure of probable D-alanine-POLY(PHOSPHORIBITOL) ligase subunit-1 from streptococcus pyogenes with ATP”. X-ray diffraction, 1 ligand (ATP), 13 pockets (best druggability 0.83).…
- PDB
- 3LGX
- Type
- protein
- Length
- 2,031 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1
- EC
- 6.1.1.13
- UniProt
- Q99ZA6
- Ligands
- ATP
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1 (EC 6.1.1.13) | protein | 508 | 32% helix, 26% strand | Q99ZA6 |
| B | D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1 (EC 6.1.1.13) | protein | 507 | 33% helix, 27% strand | Q99ZA6 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.83 | 0.84 | 104 | ATP |
| 2 | 1039 | 0.82 | 0.83 | 97 | ATP |
| 3 | 1041 | 0.82 | 0.83 | 99 | ATP |
| 4 | 1187 | 0.81 | 0.82 | 105 | ATP |
| 5 | 109 | 0.41 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 508 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 177 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LGX · Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q99ZA6 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanyl carrier protein ligase (Q99ZA6) · a predicted model of the same protein · chain D against A, TM-score 0.90
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 Q99ZA6
- Elsewhere: RCSB PDB 3LGX · PDBe 3LGX · UniProt Q99ZA6
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