Research workbench
Uncrossed Fab binding to human angiopoietin 2
Analyse Uncrossed Fab binding to human angiopoietin 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IMK
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain; Light chain
- Ligands
- NA, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain | protein | 229 | 10% helix, 50% strand | — |
| B | Heavy chain | protein | 230 | 12% helix, 50% strand | — |
| C | Light chain | protein | 213 | 6% helix, 50% strand | — |
| D | Light chain | protein | 210 | 8% helix, 52% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.76 | 0.79 | 106 | empty |
| 2 | 727 | 0.67 | 0.75 | 62 | empty |
| 3 | 317 | 0.56 | 0.76 | 35 | GOL |
| 4 | 190 | 0.51 | 0.77 | 27 | empty |
| 5 | 56 | 0.45 | 0.84 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1918 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1823 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 292 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 273 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 162 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4IMK · Uncrossed Fab binding to human Angiopoietin 2 · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 4IMK · PDBe 4IMK
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