MolNFT v1 · #156565 · protein
Fab 10A6 in complex with mpts
6M87 · Fab 10A6 light chain: “Fab 10A6 in complex with mpts”. X-ray diffraction, 2 ligands (2M9, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #156565 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6M87
- Type
- protein
- Length
- 2,548 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 10A6 light chain; Fab 10A6 heavy chain
- Ligands
- 2M9, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Fab 10A6 light chain | protein | 211 | 6% helix, 51% strand | — |
| B, F, H | Fab 10A6 heavy chain | protein | 215 | 4% helix, 52% strand | — |
| C, G | Fab 10A6 light chain | protein | 209 | 7% helix, 54% strand | — |
| I | Fab 10A6 light chain | protein | 208 | 6% helix, 50% strand | — |
| K | Fab 10A6 light chain | protein | 207 | 4% helix, 51% strand | — |
| D, J, L | Fab 10A6 heavy chain | protein | 216 | 4% helix, 54% strand | — |
Ligands and binding sites
- 2M9 · 8-methoxypyrene-1,3,6-trisulfonic acid · ligand · 6 copies · chains A, B, H, E, F, G, K, L, C, D, I, J
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, G, H, I, J, C, D, E, F, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.79 | 0.83 | 79 | 2M9, SO4 |
| 2 | 198 | 0.74 | 0.90 | 34 | 2M9 |
| 3 | 402 | 0.66 | 0.80 | 46 | SO4 |
| 4 | 708 | 0.66 | 0.75 | 62 | empty |
| 5 | 495 | 0.65 | 0.77 | 76 | empty |
Interfaces
23 interfaces between chains.
- E–F · 1864 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1863 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 1858 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 1844 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1844 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 9 modified (disulfide, cyclization).
Compared structures
- 6M87 · Fab 10A6 in complex with MPTS · 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 6M87 · PDBe 6M87
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