MolNFT v1 · #117570 · protein
Crystal structure of lysenin pore
5EC5: “Crystal structure of lysenin pore”. X-ray diffraction, 2 ligands (MBO, HG), 20 pockets (best druggability 0.81). MolNFT v1 #117570 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EC5
- Type
- protein
- Length
- 5,152 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysenin
- UniProt
- O18423
- Ligands
- MBO, HG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 1% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, J, K | Lysenin | protein | 290 | 1% helix, 64% strand | O18423 |
| B | Lysenin | protein | 284 | 1% helix, 66% strand | O18423 |
| C | Lysenin | protein | 286 | 1% helix, 65% strand | O18423 |
| D | Lysenin | protein | 285 | 1% helix, 65% strand | O18423 |
| E, H, S | Lysenin | protein | 283 | 1% helix, 65% strand | O18423 |
| F, R | Lysenin | protein | 283 | 1% helix, 66% strand | O18423 |
| I | Lysenin | protein | 282 | 1% helix, 66% strand | O18423 |
| L | Lysenin | protein | 284 | 1% helix, 67% strand | O18423 |
| M, N, O, P | Lysenin | protein | 289 | 1% helix, 66% strand | O18423 |
Ligands and binding sites
- MBO · Mercuribenzoic acid · ligand · 22 copies · chains A, B, C, D, E, F, G, H, I, K, L, M, O, P, R, S
- HG · Mercury (II) ion · metal · 14 copies · chains C, D, E, F, G, I, J, N, O, P, R, S
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 | 951 | 0.81 | 0.83 | 115 | empty |
| 2 | 644 | 0.79 | 0.84 | 99 | empty |
| 3 | 614 | 0.78 | 0.84 | 95 | empty |
| 4 | 488 | 0.76 | 0.84 | 75 | empty |
| 5 | 587 | 0.75 | 0.82 | 86 | empty |
Interfaces
34 interfaces between chains.
- M–N · 3523 Ų buried · 74 hydrogen bonds · protein-protein
- N–O · 3495 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 3476 Ų buried · 62 hydrogen bonds · protein-protein
- J–K · 3435 Ų buried · 70 hydrogen bonds · protein-protein
- O–P · 3421 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 5EC5 · Crystal structure of lysenin pore · the same entry in another collection · chain K against K, 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 O18423
- Elsewhere: RCSB PDB 5EC5 · PDBe 5EC5 · UniProt O18423
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