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Crystal structure of SEC4-GDP
Analyse Crystal structure of SEC4-GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G16
- Type
- protein
- Length
- 647 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein SEC4
- UniProt
- P07560
- Ligands
- GDP, CO
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein SEC4 | protein | 159 | 36% helix, 27% strand | P07560 |
| B | RAS-related protein SEC4 | protein | 161 | 34% helix, 26% strand | P07560 |
| C | RAS-related protein SEC4 | protein | 167 | 39% helix, 24% strand | P07560 |
| D | RAS-related protein SEC4 | protein | 160 | 38% helix, 26% strand | P07560 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.72 | 0.81 | 57 | empty |
| 2 | 434 | 0.62 | 0.77 | 65 | CO, GDP |
| 3 | 301 | 0.54 | 0.75 | 47 | CO, GDP |
| 4 | 53 | 0.49 | 0.86 | 14 | empty |
| 5 | 61 | 0.33 | 0.77 | 20 | CO, GDP |
Interfaces
4 interfaces between chains.
- C–D · 662 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 249 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 104 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 103 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
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 P07560
- Elsewhere: RCSB PDB 1G16 · PDBe 1G16 · UniProt P07560
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