Research workbench
Crystal structure analysis of the epitope of an anti-mica antibody
Analyse Crystal structure analysis of the epitope of an anti-mica antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DDM
- Type
- protein
- Length
- 519 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-mica Fab fragment light chain clone 1D5; MHC class I polypeptide-related sequence a…
- UniProt
- Q96QC4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-mica Fab fragment light chain clone 1D5 | protein | 215 | 7% helix, 53% strand | — |
| C | MHC class I polypeptide-related sequence a | protein | 88 | 7% helix, 57% strand | Q96QC4 |
| B | Anti-mica Fab fragment heavy chain clone 1D5 | protein | 216 | 8% helix, 50% strand | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.66 | 0.75 | 63 | empty |
| 2 | 246 | 0.51 | 0.75 | 39 | empty |
| 3 | 62 | 0.50 | 0.86 | 21 | empty |
| 4 | 51 | 0.37 | 0.80 | 18 | empty |
| 5 | 51 | 0.29 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1794 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 505 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 322 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6DDM · 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 6DDM · PDBe 6DDM · UniProt Q96QC4
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