MolNFT v1 · #93311 · protein
Crystal structure of rap protein complexed with competence and sporulation factor
4GYO · Response regulator aspartate phosphatase J: “Crystal structure of rap protein complexed with competence and sporulation factor”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.79). MolNFT v1 #93311 on GenesisL1: 3D…
- PDB
- 4GYO
- Type
- protein
- Length
- 726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator aspartate phosphatase J; Csf peptide
- EC
- 3.1.-.-
- UniProt
- O34327
- Ligands
- CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Response regulator aspartate phosphatase J (EC 3.1.-.-) | protein | 357 | 82% helix, 0% strand | O34327 |
| B | Response regulator aspartate phosphatase J (EC 3.1.-.-) | protein | 359 | 82% helix, 0% strand | O34327 |
| C, D | Csf peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.79 | 0.87 | 50 | empty |
| 2 | 535 | 0.77 | 0.84 | 56 | empty |
| 3 | 188 | 0.62 | 0.83 | 29 | empty |
| 4 | 245 | 0.60 | 0.80 | 32 | empty |
| 5 | 158 | 0.41 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–D · 676 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 669 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 137 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4GYO · Crystal Structure of Rap Protein Complexed with Competence and Sporulation Factor · the same entry in another collection · chain A against A, TM-score 1.00
- O34327 · AlphaFold monomer V2.0 prediction for response regulator aspartate phosphatase J (O34327) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 O34327
- Elsewhere: RCSB PDB 4GYO · PDBe 4GYO · UniProt O34327
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