Research workbench
Crystal structure of the NTF2-like domain of human G3BP1 in complex with a peptide
Analyse Crystal structure of the NTF2-like domain of human G3BP1 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FCM
- Type
- protein
- Length
- 277 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS GTPase-activating protein-binding protein 1; Nucleoporin repeat peptide
- EC
- 3.6.4.12, 3.6.4.13
- UniProt
- Q13283
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.30
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS GTPase-activating protein-binding protein 1 (EC 3.6.4.12, 3.6.4.13) | protein | 132 | 27% helix, 39% strand | Q13283 |
| B | RAS GTPase-activating protein-binding protein 1 (EC 3.6.4.12, 3.6.4.13) | protein | 135 | 28% helix, 40% strand | Q13283 |
| C, D | Nucleoporin repeat peptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.30 | 0.74 | 17 | empty |
| 2 | 52 | 0.29 | 0.75 | 16 | empty |
| 3 | 57 | 0.27 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1501 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 465 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4FCM · Crystal structure of the NTF2-like domain of human G3BP1 in complex with a peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q13283 · AlphaFold monomer V2.0 prediction for RAS GTPase-activating protein- binding protein 1… · 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 Q13283
- Elsewhere: RCSB PDB 4FCM · PDBe 4FCM · UniProt Q13283
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