Research workbench
Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima complexed with ZN2+
Analyse Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BOL
- Type
- protein
- Length
- 1,106 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methyltetrahydrofolate S-homocysteine methyltransferase
- EC
- 2.1.1.13
- UniProt
- Q9WYA5
- Ligands
- HCS, ZN, K, YT3
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-methyltetrahydrofolate S-homocysteine methyltransferase (EC 2.1.1.13) | protein | 557 | 48% helix, 15% strand | Q9WYA5 |
| B | 5-methyltetrahydrofolate S-homocysteine methyltransferase (EC 2.1.1.13) | protein | 549 | 48% helix, 14% strand | Q9WYA5 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · chains B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- YT3 · Yttrium (III) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.60 | 0.83 | 30 | ZN, K, HCS |
| 2 | 218 | 0.58 | 0.80 | 30 | K |
| 3 | 150 | 0.53 | 0.80 | 23 | empty |
| 4 | 257 | 0.52 | 0.75 | 31 | empty |
| 5 | 291 | 0.51 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1135 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3BOL · Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with… · 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 Q9WYA5
- Elsewhere: RCSB PDB 3BOL · PDBe 3BOL · UniProt Q9WYA5
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