MolNFT v1 · #120353 · protein + RNA
Structure of the GEMIN5 WD40 domain in complex with aauuuuugag
5GXI · Gem-associated protein 5: “Structure of the GEMIN5 WD40 domain in complex with aauuuuugag”. X-ray diffraction, 1 ligand (UNX), 8 pockets (best druggability 0.79). MolNFT v1 #120353 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GXI
- Type
- protein + RNA
- Length
- 671 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gem-associated protein 5; RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*GP*AP*G)-3')
- UniProt
- Q8TEQ6
- Ligands
- UNX
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gem-associated protein 5 | protein | 667 | 5% helix, 47% strand | Q8TEQ6 |
| B | RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*GP*AP*G)-3') | rna | 4 | — | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 22 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.79 | 0.81 | 64 | UNX |
| 2 | 511 | 0.75 | 0.83 | 49 | UNX |
| 3 | 126 | 0.47 | 0.78 | 17 | UNX |
| 4 | 154 | 0.46 | 0.77 | 24 | empty |
| 5 | 95 | 0.40 | 0.77 | 24 | UNX |
Interfaces
1 interface between chains.
- A–B · 494 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 5GXI · PDBe 5GXI · UniProt Q8TEQ6
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