MolNFT v1 · #124556 · protein
Crystal structure of tryptophan synthase alpha beta complex from streptococcus pneumoniae
5KIN · Tryptophan synthase alpha chain: “Crystal structure of tryptophan synthase alpha beta complex from streptococcus pneumoniae”. X-ray diffraction, 13 pockets (best druggability 0.84). MolNFT v1 #124556 on GenesisL1: 3D structure…
- PDB
- 5KIN
- Type
- protein
- Length
- 1,297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain; Tryptophan synthase beta chain
- EC
- 4.2.1.20
- UniProt
- Q97P33, Q97P32
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 247 | 45% helix, 15% strand | Q97P33 |
| B, D | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 399 | 48% helix, 18% strand | Q97P32 |
| C | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 252 | 46% helix, 16% strand | Q97P33 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.84 | 0.88 | 100 | empty |
| 2 | 694 | 0.82 | 0.86 | 81 | empty |
| 3 | 350 | 0.81 | 0.90 | 57 | empty |
| 4 | 144 | 0.66 | 0.87 | 27 | GOL |
| 5 | 153 | 0.61 | 0.84 | 26 | GOL |
Interfaces
3 interfaces between chains.
- B–D · 1818 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1327 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1283 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 5KIN · Crystal structure of tryptophan synthase alpha beta complex from Streptococcus pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00
- Q97P33 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (Q97P33) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q97P32 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain (Q97P32) · a predicted model of the same protein · chain B against A, TM-score 0.98
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
- Every structure of UniProt Q97P32
- Elsewhere: RCSB PDB 5KIN · PDBe 5KIN · UniProt Q97P33 · UniProt Q97P32
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