MolNFT v1 · #136184 · protein
Structure of cobalamin-dependent S-adenosylmethionine radical enzyme oxsb with aqua-cobalamin and S-adenosylmethionine bound
5UL4 · Oxsb protein: “Structure of cobalamin-dependent S-adenosylmethionine radical enzyme oxsb with aqua-cobalamin and…”. X-ray diffraction, 3 ligands (SF4, B12, SAM), 7 pockets (best druggability 0.76). MolNFT v1 #136184 on GenesisL1: 3D…
- PDB
- 5UL4
- Type
- protein
- Length
- 729 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxsb protein
- UniProt
- O24770
- Ligands
- SF4, B12, SAM
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxsb protein | protein | 729 | 48% helix, 14% strand | O24770 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- B12 · Cobalamin · ligand · chains A
- SAM · S-adenosylmethionine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 15 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.76 | 0.79 | 104 | SF4, B12, SAM, EDO |
| 2 | 143 | 0.75 | 0.93 | 28 | empty |
| 3 | 429 | 0.63 | 0.77 | 37 | EDO |
| 4 | 78 | 0.42 | 0.80 | 19 | empty |
| 5 | 52 | 0.34 | 0.79 | 15 | empty |
Compared structures
- 5UL4 · Structure of Cobalamin-dependent S-adenosylmethionine radical enzyme OxsB with… · the same entry in another collection · chain A against A, 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 O24770
- Elsewhere: RCSB PDB 5UL4 · PDBe 5UL4 · UniProt O24770
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