MolNFT v1 · #119221 · protein
The GTPase domains of the immunity-related IRGA6 dimerize in a parallel head-to-head fashion
5FPH · Interferon-inducible GTPase 1: “The GTPase domains of the immunity-related IRGA6 dimerize in a parallel head-to-head fashion”. X-ray diffraction, 2 ligands (GNP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #119221 on…
- PDB
- 5FPH
- Type
- protein
- Length
- 2,765 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-inducible GTPase 1
- EC
- 3.6.5.-
- UniProt
- Q9QZ85
- Ligands
- GNP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interferon-inducible GTPase 1 (EC 3.6.5.-) | protein | 395 | 53% helix, 9% strand | Q9QZ85 |
| B | Interferon-inducible GTPase 1 (EC 3.6.5.-) | protein | 396 | 53% helix, 8% strand | Q9QZ85 |
| C | Interferon-inducible GTPase 1 (EC 3.6.5.-) | protein | 389 | 54% helix, 8% strand | Q9QZ85 |
| D | Interferon-inducible GTPase 1 (EC 3.6.5.-) | protein | 396 | 55% helix, 8% strand | Q9QZ85 |
| E | Interferon-inducible GTPase 1 (EC 3.6.5.-) | protein | 396 | 54% helix, 8% strand | Q9QZ85 |
| F | Interferon-inducible GTPase 1 (EC 3.6.5.-) | protein | 394 | 54% helix, 9% strand | Q9QZ85 |
| G | Interferon-inducible GTPase 1 (EC 3.6.5.-) | protein | 399 | 53% helix, 8% strand | Q9QZ85 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, E, F, G
- MG · Magnesium ion · metal · 13 copies · chains A, B, C, D, E, F, G
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.81 | 0.82 | 69 | empty |
| 2 | 896 | 0.81 | 0.83 | 63 | empty |
| 3 | 513 | 0.74 | 0.83 | 46 | empty |
| 4 | 598 | 0.73 | 0.81 | 71 | GNP, MG |
| 5 | 1027 | 0.73 | 0.76 | 87 | empty |
Interfaces
10 interfaces between chains.
- A–B · 982 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 972 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 906 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 699 Ų buried · 3 hydrogen bonds · protein-protein
- E–G · 633 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 70 modified (engineered).
Compared structures
- 5FPH · The GTPase domains of the immunity-related Irga6 dimerize in a parallel head-to-head… · the same entry in another collection · chain G against G, TM-score 1.00
- Q9QZ85 · AlphaFold monomer V2.0 prediction for interferon-inducible GTPase 1 (Q9QZ85) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 Q9QZ85
- Elsewhere: RCSB PDB 5FPH · PDBe 5FPH · UniProt Q9QZ85
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