MolNFT v1 · #80301 · protein
Crystal structure of indole-3-glycerol phosphate synthase from brucella melitensis
3TSM: “Crystal structure of indole-3-glycerol phosphate synthase from brucella melitensis”. X-ray diffraction, 2 ligands (UNL, SO4), 4 pockets (best druggability 0.79). MolNFT v1 #80301 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3TSM
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indole-3-glycerol phosphate synthase
- EC
- 4.1.1.48
- UniProt
- Q2YRR4
- Ligands
- UNL, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 261 | 45% helix, 18% strand | Q2YRR4 |
| B | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 260 | 44% helix, 18% strand | Q2YRR4 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.79 | 0.93 | 35 | SO4, UNL |
| 2 | 402 | 0.65 | 0.79 | 35 | empty |
| 3 | 111 | 0.45 | 0.78 | 20 | GOL |
| 4 | 86 | 0.43 | 0.79 | 20 | GOL |
Interfaces
1 interface between chains.
- A–B · 1444 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3TSM · Crystal structure of Indole-3-glycerol phosphate synthase from Brucella melitensis · the same entry in another collection · chain A against A, TM-score 1.00
- Q2YRR4 · AlphaFold monomer V2.0 prediction for indole-3-glycerol phosphate synthase (Q2YRR4) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q2YRR4
- Elsewhere: RCSB PDB 3TSM · PDBe 3TSM · UniProt Q2YRR4
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