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Crystal structure of T161D duck delta 2 crystallin mutant with bound argininosuccinate
Analyse Crystal structure of T161D duck delta 2 crystallin mutant with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TJW
- Type
- protein
- Length
- 1,795 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta crystallin II
- EC
- 4.3.2.1
- UniProt
- P24058
- Ligands
- AS1
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Delta crystallin II (EC 4.3.2.1) | protein | 449 | 68% helix, 5% strand | P24058 |
| B | Delta crystallin II (EC 4.3.2.1) | protein | 448 | 69% helix, 7% strand | P24058 |
| C | Delta crystallin II (EC 4.3.2.1) | protein | 449 | 69% helix, 6% strand | P24058 |
Ligands and binding sites
- AS1 · Argininosuccinate · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.77 | 0.81 | 60 | AS1 |
| 2 | 82 | 0.77 | 0.99 | 18 | empty |
| 3 | 83 | 0.76 | 0.98 | 18 | empty |
| 4 | 682 | 0.76 | 0.81 | 52 | AS1 |
| 5 | 719 | 0.75 | 0.81 | 62 | AS1 |
Interfaces
6 interfaces between chains.
- A–C · 3915 Ų buried · 67 hydrogen bonds · protein-protein
- B–D · 3871 Ų buried · 65 hydrogen bonds · protein-protein
- A–D · 1898 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1833 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1814 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1TJW · Crystal Structure of T161D Duck Delta 2 Crystallin Mutant with bound argininosuccinate · the same entry in another collection · chain D against D, TM-score 1.00
- P24058 · AlphaFold monomer V2.0 prediction for argininosuccinate lyase (P24058) · 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 P24058
- Elsewhere: RCSB PDB 1TJW · PDBe 1TJW · UniProt P24058
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