Research workbench
Crystal structure of SEC23A/SEC24A/SEC22 complexed with a C-terminal vv sorting motif
Analyse Crystal structure of SEC23A/SEC24A/SEC22 complexed with a C-terminal vv sorting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VNF
- Type
- protein
- Length
- 1,576 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 · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23A | protein | 707 | 35% helix, 23% strand | Q15436 |
| B | Protein transport protein SEC24A | protein | 729 | 31% helix, 22% strand | O95486 |
| C | Vesicle-trafficking protein SEC22B | protein | 135 | 38% helix, 27% strand | O08547 |
| D | C-terminal vv sorting motif: val-thr-ser-val-val | protein | 5 | 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.83 | 0.84 | 109 | empty |
| 2 | 1037 | 0.82 | 0.83 | 114 | empty |
| 3 | 365 | 0.69 | 0.82 | 46 | empty |
| 4 | 275 | 0.66 | 0.82 | 28 | empty |
| 5 | 447 | 0.65 | 0.78 | 49 | empty |
Interfaces
4 interfaces between chains.
- A–B · 972 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 783 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 368 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VNF · Crystal structure of Sec23a/Sec24a/Sec22 complexed with a C-terminal VV 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 5VNF · PDBe 5VNF · UniProt Q15436 · UniProt O95486 · UniProt O08547
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