MolNFT v1 · #129822 · protein
Nanobody-bound btuf, the vitamin B12 binding protein in escherichia COLI
5OVW · Vitamin B12-binding protein: “Nanobody-bound btuf, the vitamin B12 binding protein in escherichia COLI”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #129822 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5OVW
- Type
- protein
- Length
- 2,226 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12-binding protein; Nanobody
- UniProt
- P37028
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Vitamin B12-binding protein | protein | 245 | 41% helix, 15% strand | P37028 |
| G, H, I, J, K, L | Nanobody | protein | 126 | 8% helix, 42% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains B, I, D, J, E, K, F, L, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.84 | 0.87 | 67 | empty |
| 2 | 700 | 0.84 | 0.87 | 83 | empty |
| 3 | 1075 | 0.83 | 0.84 | 103 | empty |
| 4 | 370 | 0.78 | 0.88 | 44 | empty |
| 5 | 320 | 0.76 | 0.88 | 36 | empty |
Interfaces
14 interfaces between chains.
- F–L · 1201 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 1145 Ų buried · 16 hydrogen bonds · protein-protein
- D–J · 1135 Ų buried · 14 hydrogen bonds · protein-protein
- E–K · 1126 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 1122 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- P37028 · AlphaFold monomer V2.0 prediction for vitamin B12-binding protein (P37028) · 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 P37028
- Elsewhere: RCSB PDB 5OVW · PDBe 5OVW · UniProt P37028
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