Research workbench
Crystal structure of yrbi phosphatase from escherichia COLI in a complex with ca
Analyse Crystal structure of yrbi phosphatase from escherichia COLI in a complex with ca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R8Y
- Type
- protein
- Length
- 2,887 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yrbi from escherichia COLI
- UniProt
- P67653
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H, I, J, K, L, M, N, O, P | Yrbi from escherichia COLI | protein | 181 | 36% helix, 19% strand | P67653 |
| F | Yrbi from escherichia COLI | protein | 172 | 39% helix, 20% strand | P67653 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, L, J, K, M, N, O, P
- CL · Chloride ion · ion · 16 copies · chains A, B, C, D, E, F, G, H, I, L, J, K, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.78 | 0.80 | 100 | empty |
| 2 | 1055 | 0.71 | 0.75 | 92 | empty |
| 3 | 359 | 0.69 | 0.82 | 36 | CA, CL |
| 4 | 511 | 0.65 | 0.77 | 54 | empty |
| 5 | 498 | 0.62 | 0.75 | 31 | empty |
Interfaces
36 interfaces between chains.
- J–K · 1186 Ų buried · 22 hydrogen bonds · protein-protein
- O–P · 1182 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1179 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1179 Ų buried · 21 hydrogen bonds · protein-protein
- M–N · 1176 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2R8Y · Crystal structure of YrbI phosphatase from Escherichia coli in a complex with Ca · the same entry in another collection · chain P against P, 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 P67653
- Elsewhere: RCSB PDB 2R8Y · PDBe 2R8Y · UniProt P67653
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