MolNFT v1 · #11676 · protein
Degenerate interfaces in antigen-antibody complexes
1JTP · Single-domain antibody: “Degenerate interfaces in antigen-antibody complexes”. X-ray diffraction, 1 ligand (NA), 1 pocket (best druggability 0.52). MolNFT v1 #11676 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JTP
- Type
- protein
- Length
- 526 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-domain antibody; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00703
- Ligands
- NA
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-domain antibody | protein | 135 | 9% helix, 45% strand | — |
| B | Single-domain antibody | protein | 133 | 6% helix, 48% strand | — |
| L, M | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00703 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, L, M
- FMT · Formic acid · additive · 6 copies · chains A, B, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.52 | 0.74 | 35 | NA, FMT |
Interfaces
3 interfaces between chains.
- A–L · 820 Ų buried · 12 hydrogen bonds · protein-protein
- B–M · 805 Ų buried · 8 hydrogen bonds · protein-protein
- L–M · 461 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
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 P00703
- Elsewhere: RCSB PDB 1JTP · PDBe 1JTP · UniProt P00703
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