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Crystal structure of susd homolog (NP_813570.1) from bacteroides thetaiotaomicron vpi-5482 at 1.70 a resolution
Analyse Crystal structure of susd homolog (NP_813570.1) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IHV
- Type
- protein
- Length
- 1,070 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Susd homolog
- UniProt
- Q89YS2
- Ligands
- NA, CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Susd homolog | protein | 535 | 50% helix, 6% strand | Q89YS2 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.83 | 0.85 | 97 | empty |
| 2 | 164 | 0.64 | 0.86 | 26 | NA |
| 3 | 210 | 0.62 | 0.83 | 27 | NA, EDO |
| 4 | 155 | 0.59 | 0.82 | 21 | EDO |
| 5 | 149 | 0.50 | 0.78 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3IHV · Crystal structure of SusD homolog (NP_813570.1) from Bacteroides thetaiotaomicron… · the same entry in another collection · chain A against A, 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 Q89YS2
- Elsewhere: RCSB PDB 3IHV · PDBe 3IHV · UniProt Q89YS2
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