MolNFT v1 · #79966 · protein
Crystal structures of yrda from escherichia COLI, a homologous protein of gamma-class carbonic anhydrases, show possible allosteric conformations
3TIS · Protein yrda: “Crystal structures of yrda from escherichia COLI, a homologous protein of gamma-class carbonic anhydrases…”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.76). MolNFT v1 #79966 on GenesisL1: 3D…
- PDB
- 3TIS
- Type
- protein
- Length
- 520 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein yrda
- UniProt
- P0A9W9
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein yrda | protein | 174 | 14% helix, 41% strand | P0A9W9 |
| B | Protein yrda | protein | 176 | 13% helix, 40% strand | P0A9W9 |
| C | Protein yrda | protein | 170 | 13% helix, 42% strand | P0A9W9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.76 | 0.81 | 70 | ZN |
| 2 | 61 | 0.73 | 0.99 | 26 | empty |
| 3 | 317 | 0.60 | 0.78 | 38 | empty |
| 4 | 344 | 0.60 | 0.77 | 39 | empty |
| 5 | 302 | 0.54 | 0.75 | 48 | empty |
Interfaces
3 interfaces between chains.
- B–C · 926 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 862 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3TIS · Crystal structures of yrdA from Escherichia coli, a homologous protein of gamma-class… · the same entry in another collection · chain B against B, TM-score 1.00
- P0A9W9 · AlphaFold monomer V2.0 prediction for protein yrda (P0A9W9) · a predicted model of the same protein · chain B 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 3TIS · PDBe 3TIS · UniProt P0A9W9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.