Research workbench
Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl- AMINO(DETHIA)-CoA
Analyse Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N97
- Type
- protein
- Length
- 1,560 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl-CoA decarboxylase
- EC
- 4.1.1.-
- UniProt
- P52045
- Ligands
- YZS, KGP, NI
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Methylmalonyl-CoA decarboxylase (EC 4.1.1.-) | protein | 260 | 46% helix, 16% strand | P52045 |
Ligands and binding sites
- YZS · (2S)-sulfonatepropionyl-amino(dethia)-CoA · ligand · 9 copies · chains A, B, C, D, E, F
- KGP · (2R)-sulfonatepropionyl-amino(dethia)-CoA · ligand · 6 copies · chains A, B, C, D, E, F
- NI · Nickel (II) ion · metal · 2 copies · chains A, B, C, D, E, F
- IMD · Imidazole · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.83 | 0.90 | 55 | NI |
| 2 | 485 | 0.83 | 0.90 | 56 | NI |
| 3 | 225 | 0.63 | 0.83 | 29 | empty |
| 4 | 244 | 0.62 | 0.81 | 37 | YZS, KGP |
| 5 | 252 | 0.62 | 0.80 | 37 | YZS, KGP |
Interfaces
15 interfaces between chains.
- B–C · 1729 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1728 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1718 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1707 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1704 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6N97 · Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-amino(dethia)-CoA · the same entry in another collection · chain C against C, TM-score 1.00
- P52045 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA decarboxylase (P52045) · 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 P52045
- Elsewhere: RCSB PDB 6N97 · PDBe 6N97 · UniProt P52045
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