Research workbench
Crystal structure of probable yrbi family phosphatase from pseudomonas syringae PV.PHASEOLICA 1448A
Analyse Crystal structure of probable yrbi family phosphatase from pseudomonas syringae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MN1
- Type
- protein
- Length
- 2,102 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable yrbi family phosphatase
- UniProt
- Q48EB9
- Ligands
- CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable yrbi family phosphatase | protein | 183 | 44% helix, 19% strand | Q48EB9 |
| B, C, E, I | Probable yrbi family phosphatase | protein | 174 | 44% helix, 20% strand | Q48EB9 |
| D, F, K | Probable yrbi family phosphatase | protein | 176 | 45% helix, 19% strand | Q48EB9 |
| G, H, L | Probable yrbi family phosphatase | protein | 173 | 43% helix, 20% strand | Q48EB9 |
| J | Probable yrbi family phosphatase | protein | 176 | 43% helix, 19% strand | Q48EB9 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, C, B, K, D, H, E, I, F, G, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.82 | 0.83 | 109 | CL |
| 2 | 1031 | 0.81 | 0.82 | 86 | CL |
| 3 | 613 | 0.80 | 0.86 | 64 | CL |
| 4 | 660 | 0.75 | 0.82 | 78 | empty |
| 5 | 530 | 0.74 | 0.82 | 59 | empty |
Interfaces
41 interfaces between chains.
- D–H · 1216 Ų buried · 19 hydrogen bonds · protein-protein
- K–L · 1206 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1203 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1192 Ų buried · 15 hydrogen bonds · protein-protein
- B–J · 1149 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3MN1 · Crystal structure of probable yrbi family phosphatase from pseudomonas syringae… · 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 Q48EB9
- Elsewhere: RCSB PDB 3MN1 · PDBe 3MN1 · UniProt Q48EB9
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