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
- 6DDV
- Type
- protein
- Length
- 533 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-mica Fab fragment heavy chain clone 6E1; MHC class I chain-related protein a…
- UniProt
- H9CTV0
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Anti-mica Fab fragment heavy chain clone 6E1 | protein | 222 | 10% helix, 51% strand | — |
| C | MHC class I chain-related protein a | protein | 94 | 6% helix, 65% strand | H9CTV0 |
| A | Anti-mica Fab fragment light chain clone 6E1 | protein | 217 | 6% helix, 50% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.62 | 0.74 | 69 | empty |
| 2 | 63 | 0.31 | 0.75 | 20 | empty |
| 3 | 72 | 0.30 | 0.73 | 20 | empty |
| 4 | 58 | 0.29 | 0.75 | 16 | empty |
| 5 | 50 | 0.25 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1953 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 561 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 207 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6DDV · Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody · the same entry in another collection · chain B against B, 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 H9CTV0
- Elsewhere: RCSB PDB 6DDV · PDBe 6DDV · UniProt H9CTV0
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