MolNFT v1 · #14237 · protein
Crystal structure of the yeast SEC23/24 heterodimer
1M2V · Protein transport protein SEC23: “Crystal structure of the yeast SEC23/24 heterodimer”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.78). MolNFT v1 #14237 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1M2V
- Type
- protein
- Length
- 1,453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23; Protein transport protein SEC24
- UniProt
- P15303, P40482
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23 | protein | 705 | 33% helix, 24% strand | P15303 |
| B | Protein transport protein SEC24 | protein | 748 | 32% helix, 22% strand | P40482 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.78 | 0.87 | 60 | empty |
| 2 | 223 | 0.74 | 0.89 | 29 | empty |
| 3 | 97 | 0.72 | 0.94 | 28 | empty |
| 4 | 234 | 0.62 | 0.81 | 35 | empty |
| 5 | 401 | 0.61 | 0.76 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 933 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1M2V · Crystal Structure of the yeast Sec23/24 heterodimer · the same entry in another collection · chain A against A, TM-score 1.00
- P15303 · AlphaFold monomer V2.0 prediction for protein transport protein SEC23 (P15303) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P40482 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24 (P40482) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P15303
- Every structure of UniProt P40482
- Elsewhere: RCSB PDB 1M2V · PDBe 1M2V · UniProt P15303 · UniProt P40482
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