MolNFT v1 · #15728 · protein
Crystal structure of Fab fragment of antibody hyhel-26 complexed with lysozyme
1NDM · Antibody kappa light chain: “Crystal structure of Fab fragment of antibody hyhel-26 complexed with lysozyme”. X-ray diffraction, 6 pockets (best druggability 0.57). MolNFT v1 #15728 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1NDM
- Type
- protein
- Length
- 553 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody kappa light chain; Immunoglobulin gamma 1 chain; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P01837, P01865, P00698
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody kappa light chain | protein | 214 | 6% helix, 52% strand | P01837 |
| B | Immunoglobulin gamma 1 chain | protein | 210 | 7% helix, 51% strand | P01865 |
| C | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.57 | 0.82 | 22 | empty |
| 2 | 337 | 0.53 | 0.74 | 47 | empty |
| 3 | 166 | 0.46 | 0.75 | 21 | empty |
| 4 | 103 | 0.35 | 0.74 | 22 | empty |
| 5 | 77 | 0.35 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1824 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 598 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 423 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1NDM · Crystal structure of Fab fragment of antibody HyHEL-26 complexed with lysozyme · the same entry in another collection · chain A against A, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain B against A, TM-score 0.50
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain A against A, TM-score 0.49
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 P01837
- Every structure of UniProt P01865
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1NDM · PDBe 1NDM · UniProt P01837 · UniProt P01865 · UniProt P00698
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