Research workbench
Structure of SEC23-SAR1 complexed with the active fragment of SEC31
Analyse Structure of SEC23-SAR1 complexed with the active fragment of SEC31 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QTV
- Type
- protein
- Length
- 933 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23; Small copii coat GTPase SAR1; Protein transport protein…
- EC
- 3.6.5.-
- UniProt
- P15303, P20606, P38968
- Ligands
- GNP, ZN, MG
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23 | protein | 733 | 32% helix, 25% strand | P15303 |
| B | Small copii coat GTPase SAR1 (EC 3.6.5.-) | protein | 164 | 31% helix, 22% strand | P20606 |
| D | Protein transport protein SEC31 | protein | 36 | 11% helix, 0% strand | P38968 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.77 | 0.97 | 21 | empty |
| 2 | 758 | 0.74 | 0.79 | 77 | empty |
| 3 | 405 | 0.70 | 0.82 | 48 | empty |
| 4 | 463 | 0.69 | 0.80 | 52 | MG, GNP |
| 5 | 319 | 0.66 | 0.81 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1750 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1487 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 543 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2QTV · Structure of Sec23-Sar1 complexed with the active fragment of Sec31 · 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
- P20606 · AlphaFold monomer V2.0 prediction for small copii coat GTPase SAR1 (P20606) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P38968 · AlphaFold monomer V2.0 prediction for protein transport protein SEC31 (P38968) · a predicted model of the same protein · chain D against A, TM-score 0.32
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 P20606
- Every structure of UniProt P38968
- Elsewhere: RCSB PDB 2QTV · PDBe 2QTV · UniProt P15303 · UniProt P20606 · UniProt P38968
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.