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Crystal structure of human mmachc
Analyse Crystal structure of human mmachc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SOM
- Type
- protein
- Length
- 3,659 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonic aciduria and homocystinuria type C protein
- UniProt
- Q9Y4U1
- Ligands
- 5AD, B12, DHL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 9 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, J, K | Methylmalonic aciduria and homocystinuria type C protein | protein | 227 | 40% helix, 18% strand | Q9Y4U1 |
| B, F, G, I | Methylmalonic aciduria and homocystinuria type C protein | protein | 228 | 40% helix, 18% strand | Q9Y4U1 |
| C, O | Methylmalonic aciduria and homocystinuria type C protein | protein | 228 | 41% helix, 18% strand | Q9Y4U1 |
| D | Methylmalonic aciduria and homocystinuria type C protein | protein | 229 | 41% helix, 18% strand | Q9Y4U1 |
| E | Methylmalonic aciduria and homocystinuria type C protein | protein | 230 | 41% helix, 18% strand | Q9Y4U1 |
| L | Methylmalonic aciduria and homocystinuria type C protein | protein | 231 | 40% helix, 18% strand | Q9Y4U1 |
| M | Methylmalonic aciduria and homocystinuria type C protein | protein | 231 | 40% helix, 18% strand | Q9Y4U1 |
| N | Methylmalonic aciduria and homocystinuria type C protein | protein | 232 | 42% helix, 18% strand | Q9Y4U1 |
| P | Methylmalonic aciduria and homocystinuria type C protein | protein | 230 | 40% helix, 18% strand | Q9Y4U1 |
Ligands and binding sites
- 5AD · 5'-deoxyadenosine · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- B12 · Cobalamin · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- DHL · 2-amino-ethanethiol · ligand · 14 copies · chains A, C, D, F, G, H, I, J, K, L, M, N, O, P
- FLC · Citrate anion · additive · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- EDO · 1,2-ethanediol · additive · 3 copies · chains E, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.79 | 0.81 | 65 | B12, FLC |
| 2 | 957 | 0.79 | 0.81 | 74 | B12, FLC, 5AD |
| 3 | 608 | 0.75 | 0.82 | 45 | empty |
| 4 | 918 | 0.74 | 0.78 | 66 | 5AD, B12, FLC |
| 5 | 978 | 0.74 | 0.77 | 72 | 5AD, B12, FLC |
Interfaces
31 interfaces between chains.
- E–F · 1087 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1062 Ų buried · 9 hydrogen bonds · protein-protein
- M–N · 1057 Ų buried · 7 hydrogen bonds · protein-protein
- I–J · 1055 Ų buried · 8 hydrogen bonds · protein-protein
- K–L · 1002 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 10 covalent (engineered, covalent ligand).
Compared structures
- 3SOM · crystal structure of human MMACHC · the same entry in another collection · chain K against K, 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 Q9Y4U1
- Elsewhere: RCSB PDB 3SOM · PDBe 3SOM · UniProt Q9Y4U1
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