MolNFT v1 · #146311 · protein
Crystal structure analysis of the epitope of an anti-mica antibody
6DDR · Anti-mica Fab fragment light chain clone 13A9: “Crystal structure analysis of the epitope of an anti-mica antibody”. X-ray diffraction, 2 ligands (ZN, SO4), 3 pockets (best druggability 0.53). MolNFT v1 #146311 on GenesisL1: 3D…
- PDB
- 6DDR
- Type
- protein
- Length
- 529 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-mica Fab fragment light chain clone 13A9; Anti-mica Fab fragment heavy chain clone…
- UniProt
- Q96QC4
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-mica Fab fragment light chain clone 13A9 | protein | 214 | 5% helix, 50% strand | — |
| B | Anti-mica Fab fragment heavy chain clone 13A9 | protein | 221 | 10% helix, 51% strand | — |
| C | MHC class I polypeptide-related sequence a | protein | 94 | 6% helix, 59% strand | Q96QC4 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains C
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.53 | 0.75 | 35 | GOL |
| 2 | 213 | 0.52 | 0.77 | 29 | empty |
| 3 | 67 | 0.29 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1973 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 589 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6DDR · Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody · 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
- Every structure of UniProt Q96QC4
- Elsewhere: RCSB PDB 6DDR · PDBe 6DDR · UniProt Q96QC4
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