MolNFT v1 · #93543 · protein
Crystal structure of the guanine nucleotide exchange factor SEC12 (P64 form)
4H5J · Guanine nucleotide-exchange factor SEC12: “Crystal structure of the guanine nucleotide exchange factor SEC12 (P64 form)”. X-ray diffraction, 1 ligand (K), 4 pockets (best druggability 0.74). MolNFT v1 #93543 on GenesisL1: 3D…
- PDB
- 4H5J
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-exchange factor SEC12
- UniProt
- P11655
- Ligands
- K
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-exchange factor SEC12 | protein | 343 | 3% helix, 53% strand | P11655 |
| B | Guanine nucleotide-exchange factor SEC12 | protein | 347 | 3% helix, 52% strand | P11655 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.74 | 0.83 | 67 | K |
| 2 | 180 | 0.66 | 0.86 | 38 | empty |
| 3 | 200 | 0.52 | 0.78 | 28 | empty |
| 4 | 272 | 0.52 | 0.75 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 142 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4H5J · Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P64 form) · the same entry in another collection · chain A against A, 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 1.00
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
- Elsewhere: RCSB PDB 4H5J · PDBe 4H5J · UniProt P11655
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