Research workbench
Structure of the integrin ALPHAIIBBETA3-abciximab complex
Analyse Structure of the integrin ALPHAIIBBETA3-abciximab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V4P
- Type
- protein
- Length
- 1,262 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3; Abciximab, heavy chain; Abciximab, light chain
- UniProt
- P08514, P05106
- Ligands
- CA, MG
- Pockets
- 10 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib | protein | 452 | 5% helix, 42% strand | P08514 |
| B | Integrin beta-3 | protein | 375 | 21% helix, 33% strand | P05106 |
| C | Abciximab, heavy chain | protein | 221 | 7% helix, 48% strand | — |
| D | Abciximab, light chain | protein | 214 | 5% helix, 43% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.79 | 0.81 | 75 | MG |
| 2 | 618 | 0.76 | 0.83 | 57 | empty |
| 3 | 311 | 0.54 | 0.75 | 43 | empty |
| 4 | 107 | 0.49 | 0.81 | 26 | empty |
| 5 | 167 | 0.46 | 0.76 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2012 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1831 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 591 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 518 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 123 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6V4P · Structure of the integrin AlphaIIbBeta3-Abciximab complex · 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 P08514
- Every structure of UniProt P05106
- Elsewhere: RCSB PDB 6V4P · PDBe 6V4P · UniProt P08514 · UniProt P05106
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.