MolNFT v1 · #54370 · protein
The crystal structure of LMO2642
2XMO · LMO2642 protein: “The crystal structure of LMO2642”. X-ray diffraction, 4 ligands (MN, FE, CA), 13 pockets (best druggability 0.67). MolNFT v1 #54370 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XMO
- Type
- protein
- Length
- 818 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO2642 protein
- UniProt
- Q8Y432
- Ligands
- MN, FE, CA, PO4
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LMO2642 protein | protein | 409 | 38% helix, 20% strand | Q8Y432 |
| B | LMO2642 protein | protein | 409 | 39% helix, 20% strand | Q8Y432 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.67 | 0.77 | 55 | PO4 |
| 2 | 416 | 0.62 | 0.77 | 42 | PO4 |
| 3 | 130 | 0.46 | 0.78 | 30 | empty |
| 4 | 78 | 0.41 | 0.79 | 21 | empty |
| 5 | 82 | 0.41 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 765 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2XMO · The crystal structure of Lmo2642 · the same entry in another collection · chain A against A, 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 Q8Y432
- Elsewhere: RCSB PDB 2XMO · PDBe 2XMO · UniProt Q8Y432
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