MolNFT v1 · #67804 · protein
Structure of the B12-dependent methionine synthase (meth) C-teminal half in a "his-on" conformation
3IV9: “Structure of the B12-dependent methionine synthase (meth) C-teminal half in a "his-on" conformation”. X-ray diffraction, 1 ligand (B12), 6 pockets (best druggability 0.76). MolNFT v1 #67804 on GenesisL1: 3D structure, binding sites…
- PDB
- 3IV9
- Type
- protein
- Length
- 577 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
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine synthase (EC 2.1.1.13) | protein | 577 | 45% helix, 13% strand | P13009 |
Ligands and binding sites
- B12 · Cobalamin · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.76 | 0.82 | 73 | B12 |
| 2 | 348 | 0.65 | 0.80 | 42 | empty |
| 3 | 293 | 0.61 | 0.79 | 36 | empty |
| 4 | 114 | 0.41 | 0.76 | 21 | empty |
| 5 | 54 | 0.30 | 0.76 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3IV9 · Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half in a "His-On"… · 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 0.98
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 3IV9 · PDBe 3IV9 · UniProt P13009
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