MolNFT v1 · #73338 · protein
Crystal structure of kemp elimination catalyst 1A53-2
3NYZ · Indole-3-glycerol phosphate synthase: “Crystal structure of kemp elimination catalyst 1A53-2”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.69). MolNFT v1 #73338 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3NYZ
- Type
- protein
- Length
- 494 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
- Q06121
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Indole-3-glycerol phosphate synthase (EC 4.1.1.48) | protein | 247 | 43% helix, 18% strand | Q06121 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.69 | 0.91 | 33 | SO4 |
| 2 | 109 | 0.69 | 0.91 | 31 | SO4 |
| 3 | 313 | 0.64 | 0.80 | 38 | empty |
| 4 | 56 | 0.37 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3NYZ · Crystal Structure of Kemp Elimination Catalyst 1A53-2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q06121 · AlphaFold monomer V2.0 prediction for indole-3-glycerol phosphate synthase (Q06121) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q06121
- Elsewhere: RCSB PDB 3NYZ · PDBe 3NYZ · UniProt Q06121
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