Research workbench
Meab, a bacterial homolog of mmaa, bound to gmppnp
Analyse Meab, a bacterial homolog of mmaa, bound to gmppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JYB
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl-CoA mutase accessory protein
- UniProt
- C5AP93
- Ligands
- GNP
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonyl-CoA mutase accessory protein | protein | 323 | 56% helix, 11% strand | C5AP93 |
| B | Methylmalonyl-CoA mutase accessory protein | protein | 315 | 55% helix, 11% strand | C5AP93 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.71 | 0.75 | 85 | empty |
| 2 | 85 | 0.65 | 0.91 | 19 | empty |
| 3 | 295 | 0.54 | 0.75 | 33 | empty |
| 4 | 94 | 0.53 | 0.84 | 23 | empty |
| 5 | 197 | 0.52 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2491 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4JYB · MeaB, A Bacterial Homolog of MMAA, Bound to GMPPNP · 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 C5AP93
- Elsewhere: RCSB PDB 4JYB · PDBe 4JYB · UniProt C5AP93
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