MolNFT v1 · #46236 · protein
Crystal structure of staphylococcus aureus hypothetical protein SA1388
2NYD · UPF0135 protein SA1388: “Crystal structure of staphylococcus aureus hypothetical protein SA1388”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.65). MolNFT v1 #46236 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2NYD
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0135 protein SA1388
- UniProt
- P67273
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0135 protein SA1388 | protein | 300 | 34% helix, 26% strand | P67273 |
| B | UPF0135 protein SA1388 | protein | 348 | 33% helix, 29% strand | P67273 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.65 | 0.77 | 56 | ZN |
| 2 | 341 | 0.59 | 0.77 | 47 | ZN |
| 3 | 119 | 0.42 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1872 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2NYD · Crystal structure of Staphylococcus aureus hypothetical protein SA1388 · the same entry in another collection · chain A against A, TM-score 1.00
- P67273 · AlphaFold monomer V2.0 prediction for GTP cyclohydrolase 1 type 2 homolog (P67273) · a predicted model of the same protein · chain A 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 P67273
- Elsewhere: RCSB PDB 2NYD · PDBe 2NYD · UniProt P67273
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