MolNFT v1 · #163449 · protein
Structure of D25 Fab in complex with scaffold S0_2.126
6S3D · Heavy chain: “Structure of D25 Fab in complex with scaffold S0_2.126”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #163449 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6S3D
- Type
- protein
- Length
- 1,921 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain; Light chain; S0_2.126
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Heavy chain | protein | 212 | 4% helix, 50% strand | — |
| B | Light chain | protein | 210 | 3% helix, 50% strand | — |
| C | Heavy chain | protein | 215 | 4% helix, 53% strand | — |
| D | Light chain | protein | 206 | 5% helix, 49% strand | — |
| E | Heavy chain | protein | 215 | 4% helix, 53% strand | — |
| F | Light chain | protein | 206 | 3% helix, 49% strand | — |
| L | Light chain | protein | 211 | 5% helix, 51% strand | — |
| M, O | S0_2.126 | protein | 59 | 63% helix, 3% strand | — |
| N, P | S0_2.126 | protein | 58 | 66% helix, 7% strand | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.80 | 0.82 | 107 | empty |
| 2 | 756 | 0.79 | 0.83 | 76 | empty |
| 3 | 723 | 0.77 | 0.82 | 71 | empty |
| 4 | 733 | 0.77 | 0.82 | 70 | empty |
| 5 | 683 | 0.72 | 0.79 | 77 | empty |
Interfaces
28 interfaces between chains.
- H–L · 1608 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1590 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1577 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1563 Ų buried · 12 hydrogen bonds · protein-protein
- E–O · 758 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6S3D · Structure of D25 Fab in complex with scaffold S0_2.126 · 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 6S3D · PDBe 6S3D
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