MolNFT v1 · #162869 · protein
Crystal structure of AT1412DM Fab fragment in complex with CD9 large extracellular loop
6RLO · AT1412DM Fab fragment (heavy chain): “Crystal structure of AT1412DM Fab fragment in complex with CD9 large extracellular loop”. X-ray diffraction, 3 ligands (NA, K, CL), 16 pockets (best druggability 0.68). MolNFT v1 #162869 on…
- 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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