MolNFT v1 · #54787 · protein
Crystal structure analysis of the anti-(4-hydroxy-3- nitrophenyl)-acetyl murine germline monoclonal antibody BBE6.12H3 Fab fragment in complex with a phage display derived dodecapeptide yqlrpnaetlrf
2XZQ · Anti-np murine germline monoclonal antibody BBE6.12H3…: “Crystal structure analysis of the anti-(4-hydroxy-3- nitrophenyl)-acetyl murine germline monoclonal antibody…”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability…
- PDB
- 2XZQ
- Type
- protein
- Length
- 435 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-np murine germline monoclonal antibody BBE6.12H3, heavy chain; Anti-np murine…
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-np murine germline monoclonal antibody BBE6.12H3, heavy chain | protein | 215 | 9% helix, 50% strand | — |
| L | Anti-np murine germline monoclonal antibody BBE6.12H3, light chain | protein | 211 | 8% helix, 54% strand | — |
| P | Phage display derived antigen | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains H, L, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.52 | 0.74 | 33 | ZN |
| 2 | 235 | 0.45 | 0.73 | 33 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1901 Ų buried · 13 hydrogen bonds · protein-protein
- L–P · 420 Ų buried · 10 hydrogen bonds · protein-protein
- H–P · 137 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2XZQ · Crystal structure analysis of the anti-(4-hydroxy-3-nitrophenyl)- acetyl murine germline… · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 2XZQ · PDBe 2XZQ
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