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Tryptophan synthase subunit alpha from streptococcus pneumoniae with 3D domain swap in the core of tim barrel
Analyse Tryptophan synthase subunit alpha from streptococcus pneumoniae with 3D domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QKY
- Type
- protein
- Length
- 2,522 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain
- EC
- 4.2.1.20
- UniProt
- Q97P33
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 10 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 253 | 45% helix, 15% strand | Q97P33 |
| B | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 254 | 44% helix, 15% strand | Q97P33 |
| C | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 258 | 45% helix, 14% strand | Q97P33 |
| D | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 254 | 45% helix, 15% strand | Q97P33 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 249 | 47% helix, 15% strand | Q97P33 |
| F | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 247 | 47% helix, 15% strand | Q97P33 |
| G | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 247 | 46% helix, 15% strand | Q97P33 |
| H | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 253 | 45% helix, 15% strand | Q97P33 |
| I | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 252 | 46% helix, 15% strand | Q97P33 |
| J | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 255 | 46% helix, 15% strand | Q97P33 |
Ligands and binding sites
- ACY · Acetic acid · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- GOL · Glycerol · additive · 3 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.76 | 0.80 | 84 | ACY |
| 2 | 823 | 0.76 | 0.80 | 103 | ACY |
| 3 | 694 | 0.76 | 0.81 | 83 | ACY |
| 4 | 626 | 0.72 | 0.79 | 68 | ACY |
| 5 | 425 | 0.71 | 0.82 | 46 | empty |
Interfaces
20 interfaces between chains.
- C–D · 5500 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 5499 Ų buried · 59 hydrogen bonds · protein-protein
- I–J · 5477 Ų buried · 56 hydrogen bonds · protein-protein
- E–F · 5457 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 5414 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 6QKY · Tryptophan synthase subunit alpha from Streptococcus pneumoniae with 3D domain swap in… · the same entry in another collection · chain J against J, TM-score 1.00
- Q97P33 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (Q97P33) · a predicted model of the same protein · chain F against A, TM-score 0.75
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 Q97P33
- Elsewhere: RCSB PDB 6QKY · PDBe 6QKY · UniProt Q97P33
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