MolNFT v1 · #111049 · protein
1.85 ångström crystal structure of LMO0812 from listeria monocytogenes egd-E
4YF1 · LMO0812 protein: “1.85 ångström crystal structure of LMO0812 from listeria monocytogenes egd-E”. X-ray diffraction, 1 ligand (NA), 8 pockets (best druggability 0.68). MolNFT v1 #111049 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YF1
- Type
- protein
- Length
- 614 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO0812 protein
- UniProt
- Q8Y8T2
- Ligands
- NA
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LMO0812 protein | protein | 157 | 73% helix, 0% strand | Q8Y8T2 |
| B | LMO0812 protein | protein | 157 | 71% helix, 0% strand | Q8Y8T2 |
| C | LMO0812 protein | protein | 146 | 75% helix, 0% strand | Q8Y8T2 |
| D | LMO0812 protein | protein | 154 | 72% helix, 0% strand | Q8Y8T2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.68 | 0.82 | 30 | FLC |
| 2 | 57 | 0.57 | 0.90 | 20 | empty |
| 3 | 247 | 0.55 | 0.77 | 37 | empty |
| 4 | 209 | 0.51 | 0.76 | 25 | empty |
| 5 | 204 | 0.47 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–D · 883 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 821 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 379 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4YF1 · 1.85 angstrom crystal structure of lmo0812 from Listeria monocytogenes EGD-e · the same entry in another collection · chain C against C, 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 Q8Y8T2
- Elsewhere: RCSB PDB 4YF1 · PDBe 4YF1 · UniProt Q8Y8T2
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