MolNFT v1 · #145026 · protein
Crystal structure of bril bound to an affinity matured synthetic antibody.
6CBV · Heavy chain, Fab fragment: “Crystal structure of bril bound to an affinity matured synthetic antibody.”. X-ray diffraction, 1 ligand (NA), 8 pockets (best druggability 0.64). MolNFT v1 #145026 on GenesisL1: 3D structure, binding…
- PDB
- 6CBV
- Type
- protein
- Length
- 543 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain, Fab fragment; Light chain, Fab fragment; Bril
- UniProt
- P0ABE7
- Ligands
- NA
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain, Fab fragment | protein | 227 | 8% helix, 48% strand | — |
| L | Light chain, Fab fragment | protein | 213 | 8% helix, 52% strand | — |
| B | Bril | protein | 103 | 74% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- NA · Sodium ion · metal · chains L
- GOL · Glycerol · additive · 2 copies · chains H, B, L
- FMT · Formic acid · additive · 2 copies · chains H, L, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.64 | 0.75 | 61 | empty |
| 2 | 189 | 0.49 | 0.76 | 31 | FMT |
| 3 | 92 | 0.47 | 0.80 | 17 | empty |
| 4 | 90 | 0.41 | 0.78 | 20 | empty |
| 5 | 106 | 0.37 | 0.74 | 25 | GOL |
Interfaces
3 interfaces between chains.
- H–L · 1949 Ų buried · 15 hydrogen bonds · protein-protein
- L–B · 503 Ų buried · 7 hydrogen bonds · protein-protein
- H–B · 330 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6CBV · Crystal structure of BRIL bound to an affinity matured synthetic antibody. · the same entry in another collection · chain H against H, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P0ABE7
- Elsewhere: RCSB PDB 6CBV · PDBe 6CBV · UniProt P0ABE7
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