Research workbench
Crystal structure of staphylococcus aureus protein SA1388
Analyse Crystal structure of staphylococcus aureus protein SA1388 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LNL
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0135 protein SA1388
- UniProt
- P67273
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0135 protein SA1388 | protein | 307 | 34% helix, 26% strand | P67273 |
| B | UPF0135 protein SA1388 | protein | 349 | 35% helix, 28% strand | P67273 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
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 | 467 | 0.63 | 0.77 | 60 | B3P |
| 2 | 330 | 0.59 | 0.77 | 45 | B3P |
| 3 | 106 | 0.40 | 0.76 | 20 | empty |
| 4 | 59 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1863 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3LNL · Crystal structure of Staphylococcus aureus protein SA1388 · the same entry in another collection · chain B against B, 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 3LNL · PDBe 3LNL · UniProt P67273
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