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Complex of the neisserial pora P1.4 epitope peptide and two Fab-fragments (antibody MN20B9.34)
Analyse Complex of the neisserial pora P1.4 epitope peptide and two Fab-fragments… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BRR
- Type
- protein
- Length
- 887 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MN20B9.34 anti-P1.4 antibody, Fab heavy chain; MN20B9.34 anti-P1.4 antibody, Fab light…
- UniProt
- Q51183
- Ligands
- SO4, NH2
- Pockets
- 11 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | MN20B9.34 anti-P1.4 antibody, Fab heavy chain | protein | 224 | 11% helix, 53% strand | — |
| L | MN20B9.34 anti-P1.4 antibody, Fab light chain | protein | 215 | 7% helix, 52% strand | — |
| P | Class 1 outer membrane protein variable region 2 | protein | 9 | 0% helix, 44% strand | Q51183 |
| X | MN20B9.34 anti-P1.4 antibody, Fab light chain | protein | 214 | 7% helix, 55% strand | — |
| Y | MN20B9.34 anti-P1.4 antibody, Fab heavy chain | protein | 225 | 9% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains X, Y
- NH2 · Amino group · ion · chains P, Y
- ACY · Acetic acid · additive · chains X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.61 | 0.74 | 62 | empty |
| 2 | 115 | 0.55 | 0.84 | 21 | empty |
| 3 | 59 | 0.52 | 0.87 | 21 | empty |
| 4 | 177 | 0.49 | 0.77 | 28 | ACY |
| 5 | 89 | 0.49 | 0.82 | 21 | empty |
Interfaces
7 interfaces between chains.
- H–L · 2074 Ų buried · 22 hydrogen bonds · protein-protein
- X–Y · 2035 Ų buried · 25 hydrogen bonds · protein-protein
- H–P · 445 Ų buried · 14 hydrogen bonds · protein-protein
- P–Y · 387 Ų buried · 8 hydrogen bonds · protein-protein
- H–Y · 178 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2BRR · Complex of the neisserial PorA P1.4 epitope peptide and two Fab- fragments (antibody… · 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
- Every structure of UniProt Q51183
- Elsewhere: RCSB PDB 2BRR · PDBe 2BRR · UniProt Q51183
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