Research workbench
Modular evolution and design of the protein binding interface
Analyse Modular evolution and design of the protein binding interface in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J4L
- Type
- protein
- Length
- 830 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Internalin B,REPEAT MODULES,VARIABLE lymphocyte receptor B; Interleukin-6
- UniProt
- A4L9V2, Q4G1L3, P05231
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Internalin B,REPEAT MODULES,VARIABLE lymphocyte receptor B | protein | 258 | 15% helix, 16% strand | A4L9V2, Q4G1L3 |
| B | Internalin B,REPEAT MODULES,VARIABLE lymphocyte receptor B | protein | 251 | 18% helix, 17% strand | A4L9V2, Q4G1L3 |
| C | Interleukin-6 | protein | 155 | 72% helix, 0% strand | P05231 |
| D | Interleukin-6 | protein | 166 | 67% helix, 0% strand | P05231 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.74 | 0.77 | 102 | empty |
| 2 | 454 | 0.71 | 0.82 | 70 | empty |
| 3 | 110 | 0.56 | 0.84 | 21 | empty |
| 4 | 225 | 0.50 | 0.76 | 32 | empty |
| 5 | 124 | 0.41 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1070 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1014 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 877 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 255 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 107 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
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 A4L9V2
- Every structure of UniProt Q4G1L3
- Every structure of UniProt P05231
- Elsewhere: RCSB PDB 4J4L · PDBe 4J4L · UniProt A4L9V2 · UniProt Q4G1L3 · UniProt P05231
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