MolNFT v1 · #171054 · protein
Streptococcus suis sadp mutant - N285D
6YRO: “Streptococcus suis sadp mutant - N285D”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.55). MolNFT v1 #171054 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YRO
- Type
- protein
- Length
- 1,020 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sadp
- UniProt
- G5DSS1
- Ligands
- NA
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C, E | Sadp | protein | 204 | 17% helix, 43% strand | G5DSS1 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, C, E
- GOL · Glycerol · additive · 7 copies · chains D, B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.55 | 0.74 | 50 | empty |
| 2 | 88 | 0.44 | 0.80 | 22 | empty |
| 3 | 58 | 0.44 | 0.83 | 21 | empty |
| 4 | 73 | 0.39 | 0.78 | 22 | GOL |
| 5 | 58 | 0.35 | 0.78 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–C · 412 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 402 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 195 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 97 Ų buried · 1 hydrogen bond · protein-protein
- D–A · 96 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YRO · Streptococcus suis SadP mutant - N285D · the same entry in another collection · chain D against D, 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 G5DSS1
- Elsewhere: RCSB PDB 6YRO · PDBe 6YRO · UniProt G5DSS1
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