Research workbench
Crystal structure of ruminococcus gnavus immunoglobulin binding protein in complex with 338E6 Fab
Analyse Crystal structure of ruminococcus gnavus immunoglobulin binding protein in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KPJ
- Type
- protein
- Length
- 1,265 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 338E6 Fab light chain kappa; GRAM_POS_ANCHORING domain-containing protein; 338E6 Fab…
- UniProt
- A0A2N5NGA8
- Ligands
- CA
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 338E6 Fab light chain kappa | protein | 213 | 6% helix, 51% strand | — |
| E | GRAM_POS_ANCHORING domain-containing protein | protein | 218 | 8% helix, 54% strand | A0A2N5NGA8 |
| F | GRAM_POS_ANCHORING domain-containing protein | protein | 215 | 7% helix, 53% strand | A0A2N5NGA8 |
| A | 338E6 Fab heavy chain | protein | 210 | 6% helix, 51% strand | — |
| C | 338E6 Fab heavy chain | protein | 208 | 7% helix, 50% strand | — |
| D | 338E6 Fab light chain kappa | protein | 201 | 3% helix, 49% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.64 | 0.75 | 49 | empty |
| 2 | 616 | 0.64 | 0.75 | 61 | empty |
| 3 | 467 | 0.61 | 0.75 | 72 | empty |
| 4 | 309 | 0.57 | 0.77 | 48 | empty |
| 5 | 200 | 0.50 | 0.77 | 32 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1669 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1649 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 631 Ų buried · 6 hydrogen bonds · protein-protein
- F–D · 615 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 106 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7KPJ · Crystal structure of Ruminococcus gnavus immunoglobulin binding protein in complex with… · the same entry in another collection · chain B against B, 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 A0A2N5NGA8
- Elsewhere: RCSB PDB 7KPJ · PDBe 7KPJ · UniProt A0A2N5NGA8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.