MolNFT v1 · #137399 · protein
Crystal structure of SEC23A/SEC24A/SEC22 complexed with EMP24 sorting motif
5VNE · Protein transport protein SEC23A: “Crystal structure of SEC23A/SEC24A/SEC22 complexed with EMP24 sorting motif”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #137399 on GenesisL1: 3D structure…
- PDB
- 5VNE
- Type
- protein
- Length
- 1,575 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23A; Protein transport protein SEC24A; Vesicle-trafficking…
- UniProt
- Q15436, O95486, O08547
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23A | protein | 708 | 33% helix, 23% strand | Q15436 |
| B | Protein transport protein SEC24A | protein | 729 | 29% helix, 21% strand | O95486 |
| C | Vesicle-trafficking protein SEC22B | protein | 135 | 36% helix, 27% strand | O08547 |
| D | EMP24 | protein | 3 | 0% helix, 0% strand | — |
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 | 982 | 0.83 | 0.84 | 120 | empty |
| 2 | 732 | 0.80 | 0.84 | 78 | empty |
| 3 | 408 | 0.73 | 0.83 | 53 | empty |
| 4 | 393 | 0.68 | 0.81 | 50 | empty |
| 5 | 265 | 0.68 | 0.84 | 29 | empty |
Interfaces
4 interfaces between chains.
- A–B · 953 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 685 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 328 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VNE · Crystal structure of Sec23a/Sec24a/Sec22 complexed with Emp24 sorting motif · the same entry in another collection · chain A against A, TM-score 1.00
- Q15436 · AlphaFold monomer V2.0 prediction for protein transport protein SEC23A (Q15436) · a predicted model of the same protein · chain A against A, TM-score 1.00
- O95486 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24A (O95486) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O08547 · AlphaFold monomer V2.0 prediction for vesicle-trafficking protein SEC22B (O08547) · a predicted model of the same protein · chain C 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 Q15436
- Every structure of UniProt O95486
- Every structure of UniProt O08547
- Elsewhere: RCSB PDB 5VNE · PDBe 5VNE · UniProt Q15436 · UniProt O95486 · UniProt O08547
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