MolNFT v1 · #67805 · protein
Structure of the B12-dependent methionine synthase (meth) C-teminal half with adohcy bound
3IVA: “Structure of the B12-dependent methionine synthase (meth) C-teminal half with adohcy bound”. X-ray diffraction, 3 ligands (B12, SAH, NO3), 3 pockets (best druggability 0.76). MolNFT v1 #67805 on GenesisL1: 3D structure, binding…
- PDB
- 3IVA
- Type
- protein
- Length
- 576 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine synthase
- EC
- 2.1.1.13
- UniProt
- P13009
- Ligands
- B12, SAH, NO3
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine synthase (EC 2.1.1.13) | protein | 576 | 47% helix, 13% strand | P13009 |
Ligands and binding sites
- B12 · Cobalamin · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- NO3 · Nitrate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.76 | 0.79 | 89 | B12, SAH |
| 2 | 429 | 0.66 | 0.79 | 46 | empty |
| 3 | 320 | 0.56 | 0.76 | 39 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3IVA · Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half with AdoHcy bound · the same entry in another collection · chain A against A, TM-score 1.00
- P13009 · AlphaFold monomer V2.0 prediction for methionine synthase (P13009) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P13009
- Elsewhere: RCSB PDB 3IVA · PDBe 3IVA · UniProt P13009
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