Research workbench
Structure of the guanine nucleotide exchange factor SEC12 bound to the small GTPase SAR1
Analyse Structure of the guanine nucleotide exchange factor SEC12 bound to the small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X90
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-exchange factor SEC12; Small copii coat GTPase SAR1
- EC
- 3.6.5.-
- UniProt
- P11655, P20606
- Ligands
- K
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Guanine nucleotide-exchange factor SEC12 | protein | 344 | 3% helix, 52% strand | P11655 |
| A | Small copii coat GTPase SAR1 (EC 3.6.5.-) | protein | 141 | 43% helix, 19% strand | P20606 |
Ligands and binding sites
- K · Potassium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.79 | 0.85 | 67 | empty |
| 2 | 100 | 0.35 | 0.74 | 24 | empty |
| 3 | 81 | 0.34 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 1084 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6X90 · Structure of the guanine nucleotide exchange factor Sec12 bound to the small GTPase Sar1 · the same entry in another collection · chain B against B, TM-score 1.00
- P11655 · AlphaFold monomer V2.0 prediction for guanine nucleotide-exchange factor SEC12 (P11655) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P20606 · AlphaFold monomer V2.0 prediction for small copii coat GTPase SAR1 (P20606) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P11655
- Every structure of UniProt P20606
- Elsewhere: RCSB PDB 6X90 · PDBe 6X90 · UniProt P11655 · UniProt P20606
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