Research workbench
Crystal structures of yrda from escherichia COLI, a homologous protein of gamma-class carbonic anhydrase, show possible allosteric conformations
Analyse Crystal structures of yrda from escherichia COLI, a homologous protein of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TIO
- Type
- protein
- Length
- 1,049 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein yrda
- UniProt
- P0A9W9
- Ligands
- ZN, PO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Protein yrda | protein | 176 | 13% helix, 40% strand | P0A9W9 |
| B | Protein yrda | protein | 170 | 13% helix, 41% strand | P0A9W9 |
| D | Protein yrda | protein | 174 | 11% helix, 42% strand | P0A9W9 |
| F | Protein yrda | protein | 177 | 14% helix, 38% strand | P0A9W9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C, B, D, F, E
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.82 | 0.83 | 83 | empty |
| 2 | 216 | 0.77 | 0.91 | 27 | PO4 |
| 3 | 243 | 0.75 | 0.89 | 31 | PO4 |
| 4 | 69 | 0.73 | 0.98 | 24 | PO4 |
| 5 | 67 | 0.73 | 0.98 | 25 | PO4 |
Interfaces
8 interfaces between chains.
- B–C · 926 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 923 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 898 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 859 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 848 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3TIO · Crystal structures of yrdA from Escherichia coli, a homologous protein of gamma-class… · the same entry in another collection · chain F against F, TM-score 1.00
- P0A9W9 · AlphaFold monomer V2.0 prediction for protein yrda (P0A9W9) · a predicted model of the same protein · chain D 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 P0A9W9
- Elsewhere: RCSB PDB 3TIO · PDBe 3TIO · UniProt P0A9W9
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