Research workbench
Cryoem structure of murine perforin-2 ectodomain in a pre-pore form
Analyse Cryoem structure of murine perforin-2 ectodomain in a pre-pore form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SB3
- Type
- protein
- Length
- 9,664 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage-expressed gene 1 protein
- UniProt
- A1L314
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 21% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Macrophage-expressed gene 1 protein | protein | 604 | 21% helix, 26% strand | A1L314 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, P, B, C, D, E, F, G, H, I, J, K, L, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.90 | 0.92 | 135 | empty |
| 2 | 1047 | 0.90 | 0.92 | 135 | empty |
| 3 | 1134 | 0.89 | 0.91 | 153 | empty |
| 4 | 996 | 0.89 | 0.91 | 130 | empty |
| 5 | 1035 | 0.89 | 0.91 | 134 | empty |
Interfaces
32 interfaces between chains.
- B–C · 4217 Ų buried · 47 hydrogen bonds · protein-protein
- A–P · 4176 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 4175 Ų buried · 45 hydrogen bonds · protein-protein
- H–I · 4169 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 4164 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 112 disulfide, 32 glycan (disulfide, N-glycosylation).
Compared structures
- 6SB3 · CryoEM structure of murine perforin-2 ectodomain in a pre-pore form · the same entry in another collection · chain P against P, TM-score 1.00
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 6SB3 · PDBe 6SB3 · UniProt A1L314
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