Research workbench
Structure of ALPHAMBETA2/CD11BCD18 headpiece in complex with a nanobody
Analyse Structure of ALPHAMBETA2/CD11BCD18 headpiece in complex with a nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P2D
- Type
- protein
- Length
- 1,331 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of integrin alpha-M; Integrin beta; HCD11BNB1 nanobody
- UniProt
- P11215, A0A494C0X7
- Ligands
- NAG, CA
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of integrin alpha-M | protein | 751 | 13% helix, 37% strand | P11215 |
| B | Integrin beta | protein | 459 | 23% helix, 28% strand | A0A494C0X7 |
| C | HCD11BNB1 nanobody | protein | 121 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.83 | 0.84 | 86 | empty |
| 2 | 1076 | 0.75 | 0.78 | 78 | empty |
| 3 | 442 | 0.62 | 0.76 | 43 | empty |
| 4 | 70 | 0.62 | 0.91 | 20 | empty |
| 5 | 105 | 0.53 | 0.83 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1723 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 664 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
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
- Every structure of UniProt A0A494C0X7
- Elsewhere: RCSB PDB 7P2D · PDBe 7P2D · UniProt P11215 · UniProt A0A494C0X7
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