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Crystal structure of a-domain in complex with antibody
Analyse Crystal structure of a-domain in complex with antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q3G
- Type
- protein
- Length
- 2,532 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Antibody heavy chain; Integrin alpha-M
- UniProt
- P11215
- Ligands
- CA, NA, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, F, J | Antibody light chain | protein | 220 | 5% helix, 52% strand | — |
| D, B, H, K | Antibody heavy chain | protein | 224 | 7% helix, 53% strand | — |
| G, E, I, L | Integrin alpha-M | protein | 189 | 43% helix, 22% strand | P11215 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains D, G, B, E, H, I, K, L
- NA · Sodium ion · metal · 3 copies · chains D, H
- CL · Chloride ion · ion · 5 copies · chains G, E, B, J, K
- EDO · 1,2-ethanediol · additive · 25 copies · chains C, D, H, G, F, I, A, B, K, E, J, L
- GOL · Glycerol · additive · 11 copies · chains C, D, E, H, G, A, B, J, K
- PEG · Di(hydroxyethyl)ether · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.77 | 0.79 | 110 | NA, EDO |
| 2 | 605 | 0.73 | 0.80 | 64 | GOL |
| 3 | 589 | 0.73 | 0.80 | 79 | empty |
| 4 | 515 | 0.67 | 0.78 | 67 | empty |
| 5 | 416 | 0.59 | 0.75 | 48 | empty |
Interfaces
22 interfaces between chains.
- C–D · 2142 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 2117 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2116 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 2089 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 588 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3Q3G · Crystal Structure of A-domain in complex with antibody · 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
- Every structure of UniProt P11215
- Elsewhere: RCSB PDB 3Q3G · PDBe 3Q3G · UniProt P11215
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