MolNFT v1 · #107452 · protein
Crystal structure of cbby from rhodobacter sphaeroides in complex with phosphate
4UAS · Protein cbby: “Crystal structure of cbby from rhodobacter sphaeroides in complex with phosphate”. X-ray diffraction, 3 ligands (MG, PO4, CL), 4 pockets (best druggability 0.76). MolNFT v1 #107452 on GenesisL1: 3D structure, binding…
- PDB
- 4UAS
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein cbby
- UniProt
- P95649
- Ligands
- MG, PO4, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein cbby | protein | 225 | 48% helix, 12% strand | P95649 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.76 | 0.95 | 34 | PO4, MG, CL |
| 2 | 148 | 0.74 | 0.93 | 43 | PO4, CL |
| 3 | 323 | 0.57 | 0.77 | 32 | empty |
| 4 | 231 | 0.49 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 271 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4UAS · Crystal structure of CbbY from Rhodobacter sphaeroides in complex with phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P95649 · AlphaFold monomer V2.0 prediction for protein cbby (P95649) · a predicted model of the same protein · 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 P95649
- Elsewhere: RCSB PDB 4UAS · PDBe 4UAS · UniProt P95649
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