Research workbench
Crystal structure of gmppnp-bound human GIMAP7 L100Q variant
Analyse Crystal structure of gmppnp-bound human GIMAP7 L100Q variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZJC
- Type
- protein
- Length
- 1,555 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase imap family member 7
- UniProt
- Q8NHV1
- Ligands
- GNP, MG
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase imap family member 7 | protein | 283 | 57% helix, 12% strand | Q8NHV1 |
| B | GTPase imap family member 7 | protein | 257 | 51% helix, 14% strand | Q8NHV1 |
| C | GTPase imap family member 7 | protein | 254 | 52% helix, 14% strand | Q8NHV1 |
| D | GTPase imap family member 7 | protein | 223 | 50% helix, 13% strand | Q8NHV1 |
| E | GTPase imap family member 7 | protein | 286 | 55% helix, 13% strand | Q8NHV1 |
| F | GTPase imap family member 7 | protein | 252 | 54% helix, 14% strand | Q8NHV1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.87 | 0.89 | 111 | MG, GNP |
| 2 | 611 | 0.85 | 0.90 | 84 | empty |
| 3 | 590 | 0.80 | 0.86 | 63 | MG, GNP |
| 4 | 708 | 0.79 | 0.84 | 80 | MG, GNP |
| 5 | 324 | 0.79 | 0.90 | 60 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1849 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1627 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1542 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 989 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 421 Ų buried · 5 hydrogen bonds · protein-protein
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 Q8NHV1
- Elsewhere: RCSB PDB 3ZJC · PDBe 3ZJC · UniProt Q8NHV1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.