Research workbench
Inactive mutant H162N of delta 2 crystallin with bound argininosuccinate
Analyse Inactive mutant H162N of delta 2 crystallin with bound argininosuccinate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DCN
- Type
- protein
- Length
- 1,712 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta 2 crystallin
- EC
- 4.3.2.1
- UniProt
- P24058
- Ligands
- AS1
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta 2 crystallin (EC 4.3.2.1) | protein | 424 | 66% helix, 5% strand | P24058 |
| B | Delta 2 crystallin (EC 4.3.2.1) | protein | 418 | 69% helix, 5% strand | P24058 |
| C | Delta 2 crystallin (EC 4.3.2.1) | protein | 434 | 66% helix, 5% strand | P24058 |
| D | Delta 2 crystallin (EC 4.3.2.1) | protein | 436 | 68% helix, 5% strand | P24058 |
Ligands and binding sites
- AS1 · Argininosuccinate · ligand · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.77 | 0.99 | 19 | empty |
| 2 | 79 | 0.76 | 0.98 | 18 | empty |
| 3 | 65 | 0.75 | 0.99 | 22 | empty |
| 4 | 65 | 0.74 | 0.98 | 25 | empty |
| 5 | 60 | 0.73 | 0.98 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3875 Ų buried · 65 hydrogen bonds · protein-protein
- A–C · 3868 Ų buried · 64 hydrogen bonds · protein-protein
- B–C · 1575 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1405 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1030 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1DCN · Inactive mutant H162N of delta 2 crystallin 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 A against A, TM-score 0.99
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 1DCN · PDBe 1DCN · UniProt P24058
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