Research workbench
Cryo-tomography and subtomogram averaging of SAR1-SEC23-SEC24 - fitted model.
Analyse Cryo-tomography and subtomogram averaging of SAR1-SEC23-SEC24 - fitted model. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GNI
- Type
- protein
- Length
- 1,632 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23; Protein transport protein SEC24; Small copii coat GTPase…
- EC
- 3.6.5.-
- UniProt
- P15303, P40482, P20606
- Ligands
- GNP, ZN, MG
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 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 |
| E | Protein transport protein SEC24 | protein | 735 | 31% helix, 22% strand | P40482 |
| B | Small copii coat GTPase SAR1 (EC 3.6.5.-) | protein | 164 | 31% helix, 22% strand | P20606 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, E
- MG · Magnesium ion · metal · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.77 | 0.86 | 62 | empty |
| 2 | 707 | 0.74 | 0.80 | 78 | empty |
| 3 | 454 | 0.70 | 0.81 | 54 | GNP, MG |
| 4 | 276 | 0.70 | 0.85 | 35 | empty |
| 5 | 91 | 0.69 | 0.93 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1727 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 817 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GNI · Cryo-tomography and subtomogram averaging of Sar1-Sec23-Sec24 - fitted model. · the same entry in another collection · chain A against A, TM-score 1.00
- P40482 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24 (P40482) · a predicted model of the same protein · chain E 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
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
- Every structure of UniProt P20606
- Elsewhere: RCSB PDB 6GNI · PDBe 6GNI · UniProt P15303 · UniProt P40482 · UniProt P20606
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