MolNFT v1 · #89236 · protein
Crystal structure of folate-bound corrinoid iron-sulfur protein (cfesp) in complex with its methyltransferase (metr), co-crystallized with folate and TI(III) citrate reductant
4DJF · 5-methyltetrahydrofolate CORRINOID/IRON sulfur protein…: “Crystal structure of folate-bound corrinoid iron-sulfur protein (cfesp) in complex with its methyltransferase…”. X-ray diffraction, 4 ligands (C2F, SF4, COB), 20 pockets…
- PDB
- 4DJF
- Type
- protein
- Length
- 2,052 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methyltetrahydrofolate CORRINOID/IRON sulfur protein methyltransferase…
- UniProt
- Q46389, Q07340, Q07341
- Ligands
- C2F, SF4, COB, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5-methyltetrahydrofolate CORRINOID/IRON sulfur protein methyltransferase | protein | 262 | 48% helix, 14% strand | Q46389 |
| C, E | CORRINOID/IRON-sulfur protein large subunit | protein | 441 | 42% helix, 16% strand | Q07340 |
| D, F | CORRINOID/IRON-sulfur protein small subunit | protein | 323 | 42% helix, 13% strand | Q07341 |
Ligands and binding sites
- C2F · 5-methyl-5,6,7,8-tetrahydrofolic acid · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains C, E
- COB · Co-methylcobalamin · ligand · 2 copies · chains B, C, D, A, E, F
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.80 | 0.82 | 105 | CA, SF4 |
| 2 | 1057 | 0.77 | 0.79 | 105 | empty |
| 3 | 297 | 0.75 | 0.87 | 49 | empty |
| 4 | 943 | 0.75 | 0.78 | 120 | empty |
| 5 | 603 | 0.74 | 0.81 | 83 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2418 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2352 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1481 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 535 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 490 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4DJF · Crystal structure of folate-bound corrinoid iron-sulfur protein (CFeSP) in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q07341 · AlphaFold monomer V2.0 prediction for CORRINOID/IRON-sulfur protein small subunit (Q07341) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q46389 · AlphaFold monomer V2.0 prediction for 5-METHYLTETRAHYDROFOLATE:CORRINOID/IRON-sulfur… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q07340 · AlphaFold monomer V2.0 prediction for CORRINOID/IRON-sulfur protein large subunit (Q07340) · a predicted model of the same protein · chain C against A, TM-score 0.82
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 Q46389
- Every structure of UniProt Q07340
- Every structure of UniProt Q07341
- Elsewhere: RCSB PDB 4DJF · PDBe 4DJF · UniProt Q46389 · UniProt Q07340 · UniProt Q07341
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