MolNFT v1 · #14231 · protein
Crystal structure of the SEC23-SAR1 complex
1M2O · Protein transport protein SEC23: “Crystal structure of the SEC23-SAR1 complex”. X-ray diffraction, 3 ligands (GNP, ZN, MG), 20 pockets (best druggability 0.80). MolNFT v1 #14231 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1M2O
- Type
- protein
- Length
- 1,758 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23; GTP-binding protein SAR1
- UniProt
- P15303, P20606
- Ligands
- GNP, ZN, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein transport protein SEC23 | protein | 718 | 34% helix, 23% strand | P15303 |
| B | GTP-binding protein SAR1 | protein | 164 | 31% helix, 24% strand | P20606 |
| D | GTP-binding protein SAR1 | protein | 158 | 32% helix, 18% strand | P20606 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.80 | 0.81 | 124 | empty |
| 2 | 694 | 0.78 | 0.82 | 76 | MG, GNP |
| 3 | 948 | 0.77 | 0.79 | 58 | empty |
| 4 | 786 | 0.77 | 0.81 | 87 | empty |
| 5 | 95 | 0.72 | 0.95 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1709 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1666 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 867 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1M2O · Crystal Structure of the Sec23-Sar1 complex · 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
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
- Elsewhere: RCSB PDB 1M2O · PDBe 1M2O · UniProt P15303 · UniProt P20606
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