MolNFT v1 · #163711 · protein
Crystal structure of murine perforin-2 P2 domain crystal form 1
6SB1 · Macrophage-expressed gene 1 protein: “Crystal structure of murine perforin-2 P2 domain crystal form 1”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.41). MolNFT v1 #163711 on GenesisL1: 3D structure, binding…
- PDB
- 6SB1
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage-expressed gene 1 protein
- UniProt
- A1L314
- Ligands
- CL
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrophage-expressed gene 1 protein | protein | 196 | 6% helix, 56% strand | A1L314 |
| B | Macrophage-expressed gene 1 protein | protein | 196 | 6% helix, 56% strand | A1L314 |
Ligands and binding sites
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 | 105 | 0.41 | 0.77 | 19 | empty |
| 2 | 64 | 0.36 | 0.78 | 15 | empty |
| 3 | 56 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6SB1 · Crystal structure of murine perforin-2 P2 domain crystal form 1 · the same entry in another collection · chain A against A, TM-score 1.00
- A1L314 · AlphaFold monomer V2.0 prediction for macrophage-expressed gene 1 protein (A1L314) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 A1L314
- Elsewhere: RCSB PDB 6SB1 · PDBe 6SB1 · UniProt A1L314
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