Research workbench
Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl- AMINO(DETHIA)-CoA
Analyse Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N94
- 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
- KGJ, NI, K
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Methylmalonyl-CoA decarboxylase (EC 4.1.1.-) | protein | 260 | 47% helix, 17% strand | P52045 |
Ligands and binding sites
- KGJ · [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylamino]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium · ligand · 9 copies · chains A, B, C, D, E, F
- NI · Nickel (II) ion · metal · 2 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 2 copies · chains C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C
- PG4 · Tetraethylene glycol · additive · chains C
- IMD · Imidazole · additive · chains D
- PGE · Triethylene glycol · additive · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.84 | 0.90 | 55 | NI |
| 2 | 506 | 0.83 | 0.89 | 56 | empty |
| 3 | 133 | 0.72 | 0.92 | 29 | empty |
| 4 | 94 | 0.72 | 0.95 | 30 | empty |
| 5 | 181 | 0.63 | 0.85 | 27 | empty |
Interfaces
15 interfaces between chains.
- A–C · 1735 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1728 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 1728 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1718 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1703 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6N94 · Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl-amino(dethia)-CoA · the same entry in another collection · chain B against B, 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 6N94 · PDBe 6N94 · UniProt P52045
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