Research workbench
Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_GVMDMJ)
Analyse Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_GVMDMJ) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O41
- Type
- protein
- Length
- 1,485 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Germline PGZL1_GVMDMJ light chain; Germline PGZL1_GVMDMJ heavy chain; Immunoglobulin…
- UniProt
- P19909
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A, C | Germline PGZL1_GVMDMJ light chain | protein | 213 | 7% helix, 54% strand | — |
| H | Germline PGZL1_GVMDMJ heavy chain | protein | 223 | 8% helix, 51% strand | — |
| B | Germline PGZL1_GVMDMJ heavy chain | protein | 222 | 8% helix, 54% strand | — |
| D | Germline PGZL1_GVMDMJ heavy chain | protein | 222 | 7% helix, 49% strand | — |
| M, N | Immunoglobulin G-binding protein G (domain III) | protein | 60 | 23% helix, 42% strand | P19909 |
| O | Immunoglobulin G-binding protein G (domain III) | protein | 59 | 24% helix, 46% strand | P19909 |
Ligands and binding sites
- GOL · Glycerol · additive · 13 copies · chains L, H, B, A, C, D, N, O
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 | 1155 | 0.77 | 0.79 | 114 | empty |
| 2 | 443 | 0.60 | 0.75 | 50 | GOL |
| 3 | 431 | 0.58 | 0.74 | 45 | empty |
| 4 | 291 | 0.51 | 0.74 | 31 | GOL |
| 5 | 190 | 0.49 | 0.77 | 29 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1899 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1876 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1820 Ų buried · 14 hydrogen bonds · protein-protein
- H–M · 567 Ų buried · 14 hydrogen bonds · protein-protein
- D–N · 554 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6O41 · Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ) · the same entry in another collection · chain O against O, TM-score 1.00
- P19909 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P19909) · a predicted model of the same protein · chain O against A, TM-score 0.96
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 P19909
- Elsewhere: RCSB PDB 6O41 · PDBe 6O41 · UniProt P19909
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