Research workbench
Crystal structure of DH270.1 (unliganded, single-chain fv) from the DH270 broadly neutralizing N332-glycan dependent lineage
Analyse Crystal structure of DH270.1 (unliganded, single-chain fv) from the DH270… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U0U
- Type
- protein
- Length
- 940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH270.1 single-chain variable fragment
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A, C, E | DH270.1 single-chain variable fragment | protein | 235 | 4% helix, 48% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.87 | 0.90 | 121 | empty |
| 2 | 119 | 0.51 | 0.81 | 20 | empty |
| 3 | 91 | 0.44 | 0.80 | 17 | empty |
| 4 | 96 | 0.37 | 0.75 | 16 | empty |
| 5 | 109 | 0.37 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–E · 1053 Ų buried · 9 hydrogen bonds · protein-protein
- G–A · 1017 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 640 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 294 Ų buried · 1 hydrogen bond · protein-protein
- G–E · 251 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5U0U · Crystal Structure of DH270.1 (unliganded, single-chain Fv) from the DH270 Broadly… · the same entry in another collection · chain G against G, 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 5U0U · PDBe 5U0U
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