Research workbench
Crossfab binding to human angiopoietin 2
Analyse Crossfab 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
- 4IML
- Type
- protein
- Length
- 890 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crossed heavy chain (vh-ckappa); Crossed light chain (vl-CH1)
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Crossed heavy chain (vh-ckappa) | protein | 234 | 8% helix, 50% strand | — |
| L | Crossed light chain (vl-CH1) | protein | 210 | 10% helix, 48% strand | — |
| B | Crossed light chain (vl-CH1) | protein | 212 | 7% helix, 46% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.65 | 0.74 | 56 | empty |
| 2 | 197 | 0.49 | 0.76 | 31 | empty |
| 3 | 135 | 0.44 | 0.76 | 27 | empty |
| 4 | 157 | 0.43 | 0.74 | 22 | empty |
| 5 | 108 | 0.34 | 0.73 | 21 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1903 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1879 Ų buried · 23 hydrogen bonds · protein-protein
- L–B · 153 Ų buried · 1 hydrogen bond · protein-protein
- H–A · 102 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4IML · CrossFab binding to human Angiopoietin 2 · the same entry in another collection · chain H against H, 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 4IML · PDBe 4IML
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