Research workbench
Crystal structure of human RAS-like, family 12 protein in complex with GDP
Analyse Crystal structure of human RAS-like, family 12 protein in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C5C
- Type
- protein
- Length
- 659 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-like protein 12
- UniProt
- Q9NYN1
- Ligands
- GDP, MG, UNX
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-like protein 12 | protein | 164 | 41% helix, 26% strand | Q9NYN1 |
| B | RAS-like protein 12 | protein | 167 | 40% helix, 26% strand | Q9NYN1 |
| C | RAS-like protein 12 | protein | 164 | 41% helix, 26% strand | Q9NYN1 |
| D | RAS-like protein 12 | protein | 164 | 41% helix, 26% strand | Q9NYN1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.70 | 0.78 | 74 | MG, GDP |
| 2 | 422 | 0.62 | 0.77 | 43 | MG, GDP |
| 3 | 162 | 0.52 | 0.79 | 28 | MG, GDP |
| 4 | 265 | 0.51 | 0.75 | 37 | empty |
| 5 | 128 | 0.47 | 0.78 | 27 | MG, GDP |
Interfaces
4 interfaces between chains.
- A–B · 362 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 358 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 324 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 242 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3C5C · Crystal structure of human Ras-like, family 12 protein in complex with GDP · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NYN1 · AlphaFold monomer V2.0 prediction for RAS-like protein family member 12 (Q9NYN1) · a predicted model of the same protein · chain D 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 Q9NYN1
- Elsewhere: RCSB PDB 3C5C · PDBe 3C5C · UniProt Q9NYN1
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