Research workbench
Crystal structure of the complex between CNTO888 Fab and mcp-1 mutant P8A
Analyse Crystal structure of the complex between CNTO888 Fab and mcp-1 mutant P8A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DN4
- Type
- protein
- Length
- 488 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CNTO888 light chain; CNTO888 heavy chain; C-C motif chemokine 2
- UniProt
- P13500
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | CNTO888 light chain | protein | 213 | 5% helix, 54% strand | — |
| H | CNTO888 heavy chain | protein | 214 | 7% helix, 50% strand | — |
| M | C-C motif chemokine 2 | protein | 61 | 23% helix, 28% strand | P13500 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.59 | 0.74 | 61 | GOL |
| 2 | 83 | 0.32 | 0.73 | 15 | empty |
| 3 | 85 | 0.29 | 0.72 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1774 Ų buried · 17 hydrogen bonds · protein-protein
- H–M · 459 Ų buried · 8 hydrogen bonds · protein-protein
- L–M · 374 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4DN4 · Crystal structure of the complex between cnto888 fab and mcp-1 mutant p8a · the same entry in another collection · chain L against L, TM-score 1.00
- P13500 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 2 (P13500) · a predicted model of the same protein · chain M against A, TM-score 0.93
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 P13500
- Elsewhere: RCSB PDB 4DN4 · PDBe 4DN4 · UniProt P13500
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