MolNFT v1 · #121639 · protein
Crystal structure of human germline antibody IGHV3-23/IGKV4-1
5I1D · Fab light chain: “Crystal structure of human germline antibody IGHV3-23/IGKV4-1”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.71). MolNFT v1 #121639 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5I1D
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 220 | 6% helix, 52% strand | — |
| H | Fab heavy chain | protein | 216 | 7% helix, 51% strand | — |
| A | Fab light chain | protein | 218 | 5% helix, 52% strand | — |
| B | Fab heavy chain | protein | 210 | 7% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.71 | 0.77 | 86 | SO4 |
| 2 | 519 | 0.60 | 0.74 | 54 | empty |
| 3 | 60 | 0.52 | 0.87 | 22 | empty |
| 4 | 231 | 0.51 | 0.75 | 36 | empty |
| 5 | 59 | 0.50 | 0.87 | 22 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1769 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1610 Ų buried · 12 hydrogen bonds · protein-protein
- L–A · 648 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5I1D · Crystal structure of human germline antibody IGHV3-23/IGKV4-1 · 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
- Elsewhere: RCSB PDB 5I1D · PDBe 5I1D
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