MolNFT v1 · #105292 · protein
Structure of mcyg a-pcp complexed with phenylalanyl-adenylate
4R0M · Mcyg protein: “Structure of mcyg a-pcp complexed with phenylalanyl-adenylate”. X-ray diffraction, 1 ligand (FA5), 10 pockets (best druggability 0.86). MolNFT v1 #105292 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4R0M
- Type
- protein
- Length
- 1,192 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mcyg protein
- UniProt
- A8YJW1
- Ligands
- FA5
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mcyg protein | protein | 555 | 34% helix, 24% strand | A8YJW1 |
| A | Mcyg protein | protein | 637 | 38% helix, 21% strand | A8YJW1 |
Ligands and binding sites
- FA5 · Adenosine-5'-[phenylalaninyl-phosphate] · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.86 | 0.88 | 90 | FA5 |
| 2 | 1077 | 0.85 | 0.86 | 114 | FA5 |
| 3 | 612 | 0.69 | 0.78 | 64 | empty |
| 4 | 608 | 0.69 | 0.78 | 43 | empty |
| 5 | 248 | 0.66 | 0.83 | 41 | empty |
Interfaces
1 interface between chains.
- B–A · 576 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 4R0M · Structure of McyG A-PCP complexed with phenylalanyl-adenylate · 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 A8YJW1
- Elsewhere: RCSB PDB 4R0M · PDBe 4R0M · UniProt A8YJW1
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