Research workbench
Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies
Analyse Thermodynamic and structural analyses of hydrolytic mechanism by catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DTM
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin 6D9
- UniProt
- A2NHM3, P18527
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin 6D9 | protein | 218 | 5% helix, 52% strand | A2NHM3 |
| H | Immunoglobulin 6D9 | protein | 216 | 8% helix, 54% strand | P18527 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.62 | 0.75 | 60 | empty |
| 2 | 73 | 0.49 | 0.84 | 21 | empty |
| 3 | 167 | 0.46 | 0.76 | 24 | empty |
| 4 | 97 | 0.41 | 0.77 | 18 | empty |
| 5 | 84 | 0.36 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- L–H · 1733 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2DTM · Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies · the same entry in another collection · chain L against L, TM-score 1.00
- P18527 · AlphaFold monomer V2.0 prediction for ig heavy chain V region 914 (P18527) · a predicted model of the same protein · chain H against A, TM-score 0.44
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 A2NHM3
- Every structure of UniProt P18527
- Elsewhere: RCSB PDB 2DTM · PDBe 2DTM · UniProt A2NHM3 · UniProt P18527
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