MolNFT v1 · #57534 · protein
Crystal structure of CA2+-bound form of DES3-23ALG-2DELTAGF122
3AAJ · Programmed cell death protein 6: “Crystal structure of CA2+-bound form of DES3-23ALG-2DELTAGF122”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.39). MolNFT v1 #57534 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3AAJ
- Type
- protein
- Length
- 329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 6
- UniProt
- O75340
- Ligands
- CA
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death protein 6 | protein | 167 | 60% helix, 7% strand | O75340 |
| B | Programmed cell death protein 6 | protein | 162 | 57% helix, 7% strand | O75340 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.39 | 0.74 | 19 | empty |
| 2 | 90 | 0.38 | 0.76 | 15 | empty |
| 3 | 51 | 0.29 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1507 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3AAJ · Crystal structure of Ca2+-bound form of des3-23ALG-2deltaGF122 · 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 B against A, TM-score 0.97
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
- Elsewhere: RCSB PDB 3AAJ · PDBe 3AAJ · UniProt O75340
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