MolNFT v1 · #162867 · protein
Crystal structure of AT1412DM Fab fragment
6RLM · AT1412DM Fab (heavy chain): “Crystal structure of AT1412DM Fab fragment”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.81). MolNFT v1 #162867 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RLM
- Type
- protein
- Length
- 3,466 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AT1412DM Fab (heavy chain); AT1412DM Fab (light chain)
- Ligands
- CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 10 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AT1412DM Fab (heavy chain) | protein | 216 | 7% helix, 52% strand | — |
| B, F, J, L, N, P | AT1412DM Fab (light chain) | protein | 219 | 6% helix, 52% strand | — |
| C | AT1412DM Fab (heavy chain) | protein | 214 | 7% helix, 51% strand | — |
| D, H | AT1412DM Fab (light chain) | protein | 218 | 6% helix, 52% strand | — |
| E | AT1412DM Fab (heavy chain) | protein | 221 | 9% helix, 52% strand | — |
| G | AT1412DM Fab (heavy chain) | protein | 213 | 7% helix, 52% strand | — |
| I | AT1412DM Fab (heavy chain) | protein | 220 | 5% helix, 52% strand | — |
| K | AT1412DM Fab (heavy chain) | protein | 211 | 7% helix, 53% strand | — |
| M | AT1412DM Fab (heavy chain) | protein | 215 | 6% helix, 52% strand | — |
| O | AT1412DM Fab (heavy chain) | protein | 206 | 6% helix, 52% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains C, D, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.81 | 0.83 | 101 | empty |
| 2 | 1068 | 0.75 | 0.78 | 128 | CL |
| 3 | 629 | 0.74 | 0.81 | 72 | empty |
| 4 | 738 | 0.69 | 0.76 | 92 | empty |
| 5 | 617 | 0.66 | 0.76 | 65 | empty |
Interfaces
43 interfaces between chains.
- E–F · 2091 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 2018 Ų buried · 16 hydrogen bonds · protein-protein
- M–N · 1895 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1811 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1788 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 6RLM · Crystal structure of AT1412dm Fab fragment · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6RLM · PDBe 6RLM
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