MolNFT v1 · #136224 · protein
Crystal structure of 5,10-methylenetetrahydrofolate reductase metf from haemophilus influenzae
5UME: “Crystal structure of 5,10-methylenetetrahydrofolate reductase metf from haemophilus influenzae”. X-ray diffraction, 2 ligands (FAD, SO4), 18 pockets (best druggability 0.82). MolNFT v1 #136224 on GenesisL1: 3D structure, binding…
- PDB
- 5UME
- Type
- protein
- Length
- 1,696 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5,10-methylenetetrahydrofolate reductase
- EC
- 1.5.1.20
- UniProt
- P45208
- Ligands
- FAD, SO4
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5,10-methylenetetrahydrofolate reductase (EC 1.5.1.20) | protein | 285 | 51% helix, 15% strand | P45208 |
| B | 5,10-methylenetetrahydrofolate reductase (EC 1.5.1.20) | protein | 262 | 49% helix, 16% strand | P45208 |
| C | 5,10-methylenetetrahydrofolate reductase (EC 1.5.1.20) | protein | 286 | 50% helix, 15% strand | P45208 |
| D | 5,10-methylenetetrahydrofolate reductase (EC 1.5.1.20) | protein | 289 | 50% helix, 14% strand | P45208 |
| E | 5,10-methylenetetrahydrofolate reductase (EC 1.5.1.20) | protein | 292 | 49% helix, 13% strand | P45208 |
| F | 5,10-methylenetetrahydrofolate reductase (EC 1.5.1.20) | protein | 282 | 48% helix, 15% strand | P45208 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACY · Acetic acid · additive · 9 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 4 copies · chains B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.82 | 0.83 | 139 | empty |
| 2 | 801 | 0.79 | 0.83 | 83 | FAD, ACY |
| 3 | 670 | 0.78 | 0.83 | 79 | FAD, ACY |
| 4 | 565 | 0.77 | 0.84 | 59 | empty |
| 5 | 764 | 0.75 | 0.80 | 58 | FAD, ACY |
Interfaces
14 interfaces between chains.
- A–D · 2013 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1982 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1192 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 765 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 761 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5UME · Crystal Structure of 5,10-Methylenetetrahydrofolate Reductase MetF from Haemophilus… · the same entry in another collection · chain F against F, TM-score 1.00
- P45208 · AlphaFold monomer V2.0 prediction for 5,10-methylenetetrahydrofolate reductase (P45208) · a predicted model of the same protein · chain C 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 P45208
- Elsewhere: RCSB PDB 5UME · PDBe 5UME · UniProt P45208
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