Research workbench
X-ray crystal structure of putative human RAS-related GTP binding D in complex with gmppnp
Analyse X-ray crystal structure of putative human RAS-related GTP binding D in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q3F
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related GTP-binding protein D
- UniProt
- Q9NQL2
- Ligands
- GNP, MG
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related GTP-binding protein D | protein | 179 | 40% helix, 21% strand | Q9NQL2 |
| B | RAS-related GTP-binding protein D | protein | 178 | 39% helix, 20% strand | Q9NQL2 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.48 | 0.82 | 17 | empty |
| 2 | 124 | 0.46 | 0.78 | 25 | MG, GNP |
| 3 | 117 | 0.41 | 0.76 | 24 | MG, GNP |
| 4 | 78 | 0.35 | 0.74 | 13 | empty |
| 5 | 56 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 743 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2Q3F · X-ray crystal structure of putative human Ras-related GTP binding D in complex with GMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQL2 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein D (Q9NQL2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9NQL2
- Elsewhere: RCSB PDB 2Q3F · PDBe 2Q3F · UniProt Q9NQL2
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