Research workbench
Crystal structure of the dimeric BH1-Fab variant [hc-Y33W,HC-D98F,HC- G99M,LC-S30BR]
Analyse Crystal structure of the dimeric BH1-Fab variant [hc-Y33W,HC-D98F,HC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MY5
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-VEGF-a Fab fragment BH1 heavy chain; Anti-VEGF-a Fab fragment BH1 light chain
- UniProt
- V9HW68, Q7Z3Y4
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-VEGF-a Fab fragment BH1 heavy chain | protein | 222 | 8% helix, 49% strand | V9HW68 |
| L, B | Anti-VEGF-a Fab fragment BH1 light chain | protein | 218 | 6% helix, 50% strand | Q7Z3Y4 |
| A | Anti-VEGF-a Fab fragment BH1 heavy chain | protein | 221 | 8% helix, 49% strand | V9HW68 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains H, L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.64 | 0.75 | 67 | EDO |
| 2 | 660 | 0.64 | 0.74 | 74 | EDO |
| 3 | 285 | 0.58 | 0.78 | 36 | EDO |
| 4 | 63 | 0.56 | 0.89 | 20 | empty |
| 5 | 112 | 0.54 | 0.83 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2056 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 2045 Ų buried · 20 hydrogen bonds · protein-protein
- L–B · 605 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 557 Ų buried · 5 hydrogen bonds · protein-protein
- H–B · 324 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MY5 · Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR] · 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
- Every structure of UniProt V9HW68
- Every structure of UniProt Q7Z3Y4
- Elsewhere: RCSB PDB 6MY5 · PDBe 6MY5 · UniProt V9HW68 · UniProt Q7Z3Y4
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