MolNFT v1 · #159673 · protein
Structure of mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin
6OXD · Methylmalonyl-CoA mutase large subunit: “Structure of mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin”. X-ray diffraction, 4 ligands (B12, 5AD, NJS), 12 pockets (best druggability 0.89). MolNFT v1 #159673…
- PDB
- 6OXD
- Type
- protein
- Length
- 1,326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl-CoA mutase large subunit; Methylmalonyl-CoA mutase small subunit
- EC
- 5.4.99.2
- UniProt
- A0A0E8UW09, A0A045IZR3
- Ligands
- B12, 5AD, NJS, K
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonyl-CoA mutase large subunit (EC 5.4.99.2) | protein | 736 | 52% helix, 10% strand | A0A0E8UW09 |
| B | Methylmalonyl-CoA mutase small subunit (EC 5.4.99.2) | protein | 590 | 47% helix, 12% strand | A0A045IZR3 |
Ligands and binding sites
- B12 · Cobalamin · ligand · chains A
- 5AD · 5'-deoxyadenosine · ligand · chains A
- NJS · Itaconyl coenzyme A · ligand · chains A, B
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.89 | 0.91 | 138 | B12, 5AD, NJS |
| 2 | 798 | 0.77 | 0.81 | 101 | empty |
| 3 | 557 | 0.69 | 0.79 | 64 | empty |
| 4 | 443 | 0.68 | 0.80 | 45 | empty |
| 5 | 263 | 0.67 | 0.83 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 4597 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 6OXD · Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin · the same entry in another collection · chain B against B, 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 A0A0E8UW09
- Every structure of UniProt A0A045IZR3
- Elsewhere: RCSB PDB 6OXD · PDBe 6OXD · UniProt A0A0E8UW09 · UniProt A0A045IZR3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.