MolNFT v1 · #37561 · protein
Crystal structure of the anti-bax monoclonal antibody 6A7 and a bax peptide.
2G5B · 6A7 Fab light chain: “Crystal structure of the anti-bax monoclonal antibody 6A7 and a bax peptide.”. X-ray diffraction, 5 ligands (NAG, BMA, NDG), 20 pockets (best druggability 0.73). MolNFT v1 #37561 on GenesisL1: 3D structure…
- PDB
- 2G5B
- Type
- protein
- Length
- 1,760 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6A7 Fab light chain; 6A7 Fab heavy chain; Bax peptide
- UniProt
- Q58EU4, P84751
- Ligands
- NAG, BMA, NDG, MAN, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | 6A7 Fab light chain | protein | 217 | 6% helix, 52% strand | Q58EU4 |
| B, D, F, H | 6A7 Fab heavy chain | protein | 216 | 10% helix, 52% strand | P84751 |
| I, J, K, L | Bax peptide | protein | 7 | 43% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D, F, H
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains D, H
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains D
- MAN · alpha-D-mannopyranose · sugar · chains F
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.73 | 0.77 | 93 | empty |
| 2 | 546 | 0.73 | 0.81 | 76 | empty |
| 3 | 925 | 0.72 | 0.76 | 95 | empty |
| 4 | 776 | 0.69 | 0.76 | 83 | empty |
| 5 | 231 | 0.65 | 0.84 | 30 | empty |
Interfaces
19 interfaces between chains.
- C–D · 1846 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1835 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1825 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1807 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 1166 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2G5B · Crystal Structure of the anti-Bax monoclonal antibody 6A7 and a Bax peptide. · the same entry in another collection · chain L against L, 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 Q58EU4
- Every structure of UniProt P84751
- Elsewhere: RCSB PDB 2G5B · PDBe 2G5B · UniProt Q58EU4 · UniProt P84751
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