MolNFT v1 · #28222 · protein
Crystal structure of the B. subtilis ykud protein at 2 a resolution
1Y7M · Hypothetical protein BSU14040: “Crystal structure of the B. subtilis ykud protein at 2 a resolution”. X-ray diffraction, 2 ligands (CD, SO4), 4 pockets (best druggability 0.68). MolNFT v1 #28222 on GenesisL1: 3D structure, binding…
- PDB
- 1Y7M
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein BSU14040
- UniProt
- O34816
- Ligands
- CD, SO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein BSU14040 | protein | 164 | 20% helix, 37% strand | O34816 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.68 | 0.79 | 46 | SO4 |
| 2 | 220 | 0.63 | 0.83 | 41 | empty |
| 3 | 74 | 0.48 | 0.83 | 14 | empty |
| 4 | 62 | 0.29 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 922 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1Y7M · Crystal Structure of the B. subtilis YkuD protein at 2 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- O34816 · AlphaFold monomer V2.0 prediction for putative L,D-transpeptidase ykud (O34816) · 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 O34816
- Elsewhere: RCSB PDB 1Y7M · PDBe 1Y7M · UniProt O34816
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