MolNFT v1 · #121636 · protein
Crystal structure of human germline antibody IGHV3-23/IGKV3-11
5I1A · CNTO388 light chain: “Crystal structure of human germline antibody IGHV3-23/IGKV3-11”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.69). MolNFT v1 #121636 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5I1A
- Type
- protein
- Length
- 862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CNTO388 light chain; CNTO388 heavy chain
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | CNTO388 light chain | protein | 212 | 7% helix, 51% strand | — |
| H | CNTO388 heavy chain | protein | 220 | 10% helix, 50% strand | — |
| A | CNTO388 light chain | protein | 211 | 7% helix, 51% strand | — |
| B | CNTO388 heavy chain | protein | 219 | 10% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains L, A, H, B
- GOL · Glycerol · additive · 2 copies · chains B, A
- ACT · Acetate ion · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.69 | 0.74 | 94 | SO4 |
| 2 | 533 | 0.60 | 0.74 | 53 | empty |
| 3 | 56 | 0.49 | 0.86 | 19 | GOL |
| 4 | 52 | 0.44 | 0.84 | 21 | empty |
| 5 | 83 | 0.34 | 0.75 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1936 Ų buried · 19 hydrogen bonds · protein-protein
- L–H · 1903 Ų buried · 15 hydrogen bonds · protein-protein
- L–A · 577 Ų buried · 3 hydrogen bonds · protein-protein
- H–A · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5I1A · Crystal structure of human germline antibody IGHV3-23/IGKV3-11 · 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 5I1A · PDBe 5I1A
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