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Crystal structure of uroporphyrin-III C-methyl transferase from thermus thermophilus complexed with S-adenyl homocysteine
Analyse Crystal structure of uroporphyrin-III C-methyl transferase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V9A
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uroporphyrin-III C-methyltransferase
- EC
- 2.1.1.107
- UniProt
- Q5SKH6
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 219 | 29% helix, 26% strand | Q5SKH6 |
| B | Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) | protein | 228 | 25% helix, 26% strand | Q5SKH6 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.75 | 0.84 | 56 | FLC, SAH |
| 2 | 512 | 0.74 | 0.82 | 55 | SAH |
| 3 | 267 | 0.57 | 0.77 | 34 | empty |
| 4 | 125 | 0.41 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2330 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1V9A · Crystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus… · 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 Q5SKH6
- Elsewhere: RCSB PDB 1V9A · PDBe 1V9A · UniProt Q5SKH6
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