MolNFT v1 · #141182 · protein
The cystathionine-beta-synthase (cbs) domain of magnesium and cobalt efflux protein corc in complex with both C2'- and C3'-endo AMP
5YZ2: “The cystathionine-beta-synthase (cbs) domain of magnesium and cobalt efflux protein corc in complex with both…”. X-ray diffraction, 1 ligand (AMP), 1 pocket (best druggability 0.70). MolNFT v1 #141182 on GenesisL1: 3D structure…
- PDB
- 5YZ2
- Type
- protein
- Length
- 267 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Magnesium and cobalt efflux protein corc
- UniProt
- P0AE78
- Ligands
- AMP
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Magnesium and cobalt efflux protein corc | protein | 131 | 43% helix, 24% strand | P0AE78 |
| B | Magnesium and cobalt efflux protein corc | protein | 136 | 45% helix, 24% strand | P0AE78 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.70 | 0.77 | 71 | AMP |
Interfaces
1 interface between chains.
- A–B · 1240 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5YZ2 · the cystathionine-beta-synthase (CBS) domain of magnesium and cobalt efflux protein CorC… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AE78 · AlphaFold monomer V2.0 prediction for magnesium and cobalt efflux protein corc (P0AE78) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P0AE78
- Elsewhere: RCSB PDB 5YZ2 · PDBe 5YZ2 · UniProt P0AE78
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