Research workbench
The crystal structure of siab-siac complex from pseudomonas aeruginosa
Analyse The crystal structure of siab-siac complex from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KKO
- Type
- protein
- Length
- 591 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative serine phosphatase; DUF1987 domain-containing protein
- UniProt
- A0A485GYA3, A0A072ZHB4
- Ligands
- ADP, NA
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative serine phosphatase | protein | 170 | 51% helix, 24% strand | A0A485GYA3 |
| B | Putative serine phosphatase | protein | 168 | 54% helix, 23% strand | A0A485GYA3 |
| C | DUF1987 domain-containing protein | protein | 127 | 37% helix, 31% strand | A0A072ZHB4 |
| D | DUF1987 domain-containing protein | protein | 126 | 37% helix, 32% strand | A0A072ZHB4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C, B, D
- NA · Sodium ion · metal · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.63 | 0.86 | 25 | empty |
| 2 | 117 | 0.60 | 0.86 | 20 | empty |
| 3 | 222 | 0.56 | 0.78 | 26 | ADP, NA |
| 4 | 231 | 0.56 | 0.78 | 27 | ADP, NA |
| 5 | 183 | 0.52 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2056 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1271 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1148 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered, phosphorylation).
Compared structures
- 6KKO · The crystal structure of SiaB-SiaC complex from Pseudomonas aeruginosa · 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 A0A485GYA3
- Every structure of UniProt A0A072ZHB4
- Elsewhere: RCSB PDB 6KKO · PDBe 6KKO · UniProt A0A485GYA3 · UniProt A0A072ZHB4
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