MolNFT v1 · #83921 · protein
X-ray crystal structural analysis of the complex between alg-2 and SEC31A peptide
3WXA · Programmed cell death protein 6: “X-ray crystal structural analysis of the complex between alg-2 and SEC31A peptide”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.47). MolNFT v1 #83921 on GenesisL1: 3D structure…
- PDB
- 3WXA
- Type
- protein
- Length
- 358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 6; Protein transport protein SEC31A
- UniProt
- O75340, O94979
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Programmed cell death protein 6 | protein | 167 | 57% helix, 8% strand | O75340 |
| C, D | Protein transport protein SEC31A | protein | 12 | 0% helix, 17% strand | O94979 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.47 | 0.76 | 26 | empty |
| 2 | 67 | 0.33 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1530 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 534 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3WXA · X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide · the same entry in another collection · chain A against A, TM-score 1.00
- O75340 · AlphaFold monomer V2.0 prediction for programmed cell death protein 6 (O75340) · a predicted model of the same protein · chain A against A, TM-score 0.93
- O94979 · AlphaFold monomer V2.0 prediction for protein transport protein SEC31A (O94979) · a predicted model of the same protein · chain C against A, TM-score 0.30
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 O75340
- Every structure of UniProt O94979
- Elsewhere: RCSB PDB 3WXA · PDBe 3WXA · UniProt O75340 · UniProt O94979
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