Research workbench
Crystal structure of AT1412DM Fab fragment in complex with CD9 large extracellular loop
Analyse Crystal structure of AT1412DM Fab fragment in complex with CD9 large… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RLO
- Type
- protein
- Length
- 2,027 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AT1412DM Fab fragment (heavy chain); AT1412DM Fab fragment (light chain); CD9 antigen
- UniProt
- P21926
- Ligands
- NA, K, CL
- Pockets
- 16 · best druggability 0.68
Structure
x-ray diffraction · 8 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | AT1412DM Fab fragment (heavy chain) | protein | 211 | 9% helix, 52% strand | — |
| B | AT1412DM Fab fragment (light chain) | protein | 219 | 6% helix, 52% strand | — |
| I, K | CD9 antigen | protein | 77 | 62% helix, 0% strand | P21926 |
| D, H | AT1412DM Fab fragment (light chain) | protein | 218 | 6% helix, 52% strand | — |
| J, L | CD9 antigen | protein | 78 | 62% helix, 0% strand | P21926 |
| E | AT1412DM Fab fragment (heavy chain) | protein | 211 | 9% helix, 52% strand | — |
| F | AT1412DM Fab fragment (light chain) | protein | 217 | 6% helix, 52% strand | — |
| G | AT1412DM Fab fragment (heavy chain) | protein | 212 | 8% helix, 53% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains B, C, D, E, F
- K · Potassium ion · metal · chains B, D
- CL · Chloride ion · ion · 11 copies · chains A, B, I, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.68 | 0.78 | 62 | empty |
| 2 | 795 | 0.67 | 0.75 | 103 | empty |
| 3 | 726 | 0.66 | 0.75 | 79 | empty |
| 4 | 506 | 0.66 | 0.77 | 59 | empty |
| 5 | 682 | 0.66 | 0.75 | 60 | NA, CL |
Interfaces
24 interfaces between chains.
- G–H · 1817 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1806 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1795 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1769 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1208 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6RLO · Crystal structure of AT1412dm Fab fragment in complex with CD9 large extracellular loop · 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 P21926
- Elsewhere: RCSB PDB 6RLO · PDBe 6RLO · UniProt P21926
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