MolNFT v1 · #134755 · protein
Crystal structure of GEMIN5 WD40 repeats in complex with M7GPPPG
5TEF · Gem-associated protein 5: “Crystal structure of GEMIN5 WD40 repeats in complex with M7GPPPG”. X-ray diffraction, 2 ligands (GTG, UNX), 6 pockets (best druggability 0.79). MolNFT v1 #134755 on GenesisL1: 3D structure, binding sites…
- PDB
- 5TEF
- Type
- protein
- Length
- 680 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gem-associated protein 5
- UniProt
- Q8TEQ6
- Ligands
- GTG, UNX
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gem-associated protein 5 | protein | 680 | 4% helix, 46% strand | Q8TEQ6 |
Ligands and binding sites
- GTG · 7-methyl-guanosine-5'-triphosphate-5'-guanosine · ligand · chains A
- UNX · Unknown atom or ion · ion · 19 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.79 | 0.81 | 66 | GTG, UNX |
| 2 | 511 | 0.76 | 0.84 | 52 | GOL, UNX |
| 3 | 381 | 0.60 | 0.76 | 40 | UNX |
| 4 | 149 | 0.46 | 0.76 | 21 | empty |
| 5 | 93 | 0.40 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5TEF · Crystal structure of Gemin5 WD40 repeats in complex with m7GpppG · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TEQ6 · AlphaFold monomer V2.0 prediction for gem-associated protein 5 (Q8TEQ6) · a predicted model of the same protein · chain A 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 Q8TEQ6
- Elsewhere: RCSB PDB 5TEF · PDBe 5TEF · UniProt Q8TEQ6
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