Research workbench
1.95 ångström resolution crystal structure of 3-deoxy-D-manno- octulosonate 8-phosphate phosphatase from yersinia pestis
Analyse 1.95 ångström resolution crystal structure of 3-deoxy-D-manno- octulosonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IJ5
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
- EC
- 3.1.3.45
- UniProt
- Q8ZB47
- Ligands
- CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45) | protein | 185 | 36% helix, 21% strand | Q8ZB47 |
| C | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45) | protein | 179 | 37% helix, 21% strand | Q8ZB47 |
| D | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45) | protein | 183 | 36% helix, 21% strand | Q8ZB47 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.72 | 0.79 | 93 | CL |
| 2 | 294 | 0.69 | 0.84 | 34 | CL |
| 3 | 209 | 0.58 | 0.80 | 24 | CL |
| 4 | 65 | 0.47 | 0.83 | 9 | empty |
| 5 | 72 | 0.42 | 0.80 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1162 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1080 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1074 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1052 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IJ5 · 1.95 Angstrom Resolution Crystal Structure of 3-deoxy-D-manno-octulosonate 8-phosphate… · the same entry in another collection · chain B against B, TM-score 1.00
- Q8ZB47 · AlphaFold monomer V2.0 prediction for 3-deoxy-D-manno-octulosonate 8-phosphate… · a predicted model of the same protein · chain C 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 Q8ZB47
- Elsewhere: RCSB PDB 3IJ5 · PDBe 3IJ5 · UniProt Q8ZB47
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