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Crystal structure analysis of an anti-lysozyme antibody
Analyse Crystal structure analysis of an anti-lysozyme antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P2C
- Type
- protein
- Length
- 1,102 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain anti-lysozyme antibody F10.6.6; Heavy chain VH+CH1 anti-lysozyme antibody…
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain anti-lysozyme antibody F10.6.6 | protein | 212 | 7% helix, 51% strand | — |
| B | Heavy chain VH+CH1 anti-lysozyme antibody F10.6.6 | protein | 210 | 6% helix, 53% strand | — |
| C, F | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
| D | Light chain anti-lysozyme antibody F10.6.6 | protein | 211 | 7% helix, 51% strand | — |
| E | Heavy chain VH+CH1 anti-lysozyme antibody F10.6.6 | protein | 211 | 7% helix, 54% strand | — |
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 | 602 | 0.62 | 0.74 | 62 | empty |
| 2 | 592 | 0.61 | 0.74 | 67 | empty |
| 3 | 86 | 0.34 | 0.74 | 18 | empty |
| 4 | 81 | 0.33 | 0.74 | 19 | empty |
| 5 | 60 | 0.30 | 0.75 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1804 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1783 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 537 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 522 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 315 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1P2C · crystal structure analysis of an anti-lysozyme antibody · the same entry in another collection · chain A against A, 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
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 1P2C · PDBe 1P2C · UniProt P00698
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