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Structure of probable D-alanine--POLY(PHOSPHORIBITOL) ligase subunit-1 from streptococcus pyogenes
Analyse Structure of probable D-alanine--POLY(PHOSPHORIBITOL) ligase subunit-1 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L8C
- Type
- protein
- Length
- 1,009 residues
- Chains
- 2
- 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
- Q5XBN5
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1 (EC 6.1.1.13) | protein | 499 | 34% helix, 25% strand | Q5XBN5 |
| B | D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1 (EC 6.1.1.13) | protein | 510 | 32% helix, 26% strand | Q5XBN5 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.84 | 0.85 | 96 | empty |
| 2 | 1130 | 0.81 | 0.82 | 96 | empty |
| 3 | 207 | 0.57 | 0.80 | 36 | empty |
| 4 | 58 | 0.35 | 0.77 | 14 | empty |
| 5 | 53 | 0.24 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 991 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3L8C · Structure of probable D-alanine--poly(phosphoribitol) ligase subunit-1 from Streptococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5XBN5 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanyl carrier protein ligase (Q5XBN5) · a predicted model of the same protein · chain B 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 Q5XBN5
- Elsewhere: RCSB PDB 3L8C · PDBe 3L8C · UniProt Q5XBN5
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