Research workbench
Monomeric polcalcin (phl P 7) in complex with two identical allergen- specific antibodies
Analyse Monomeric polcalcin (phl P 7) in complex with two identical allergen- specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OTJ
- Type
- protein
- Length
- 1,009 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 102.1F10 Fab light chain; 102.1F10 Fab heavy chain; Polcalcin phl P 7
- UniProt
- O82040
- Ligands
- CA
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | 102.1F10 Fab light chain | protein | 214 | 7% helix, 49% strand | — |
| H, B | 102.1F10 Fab heavy chain | protein | 222 | 7% helix, 55% strand | — |
| D | Polcalcin phl P 7 | protein | 68 | 59% helix, 6% strand | O82040 |
| C | Polcalcin phl P 7 | protein | 69 | 57% helix, 6% strand | O82040 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains D, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains H, A, L, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.69 | 0.76 | 57 | EDO |
| 2 | 643 | 0.65 | 0.75 | 72 | empty |
| 3 | 405 | 0.57 | 0.74 | 45 | empty |
| 4 | 164 | 0.51 | 0.78 | 21 | empty |
| 5 | 146 | 0.48 | 0.77 | 21 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1728 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1686 Ų buried · 18 hydrogen bonds · protein-protein
- H–C · 683 Ų buried · 10 hydrogen bonds · protein-protein
- D–B · 682 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 411 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5OTJ · Monomeric polcalcin (Phl p 7) in complex with two identical allergen-specific antibodies · the same entry in another collection · chain C against C, TM-score 1.00
- O82040 · AlphaFold monomer V2.0 prediction for polcalcin phl P 7 (O82040) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 O82040
- Elsewhere: RCSB PDB 5OTJ · PDBe 5OTJ · UniProt O82040
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