Research workbench
Cryoem structure of murine perforin-2 ectodomain in a pore form
Analyse Cryoem structure of murine perforin-2 ectodomain in a pore form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SB5
- Type
- protein
- Length
- 8,688 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 0.81
Structure
electron microscopy · 1 distinct chain · 12% helix, 31% 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 | 543 | 12% helix, 31% strand | A1L314 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 1005 | 0.81 | 0.82 | 127 | empty |
| 2 | 748 | 0.81 | 0.84 | 106 | empty |
| 3 | 975 | 0.81 | 0.82 | 112 | empty |
| 4 | 1098 | 0.81 | 0.82 | 132 | empty |
| 5 | 1067 | 0.80 | 0.82 | 123 | empty |
Interfaces
16 interfaces between chains.
- H–I · 3876 Ų buried · 68 hydrogen bonds · protein-protein
- L–M · 3781 Ų buried · 60 hydrogen bonds · protein-protein
- E–F · 3778 Ų buried · 63 hydrogen bonds · protein-protein
- F–G · 3760 Ų buried · 61 hydrogen bonds · protein-protein
- O–P · 3756 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 glycan, 16 disulfide (N-glycosylation, disulfide).
Compared structures
- 6SB5 · CryoEM structure of murine perforin-2 ectodomain in a 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 6SB5 · PDBe 6SB5 · UniProt A1L314
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