Research workbench
Crystal structure of Z004 igl Fab in complex with zikv ediii
Analyse Crystal structure of Z004 igl Fab in complex with zikv ediii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UTA
- Type
- protein
- Length
- 1,061 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Z004 igl Fab heavy chain; Z004 igl Fab light chain; Env
- UniProt
- S6C4S0, P0DOX7, A0A1X9PPI0
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Z004 igl Fab heavy chain | protein | 221 | 1% helix, 47% strand | S6C4S0 |
| L, B | Z004 igl Fab light chain | protein | 212 | 5% helix, 48% strand | P0DOX7 |
| E | Env | protein | 99 | 0% helix, 40% strand | A0A1X9PPI0 |
| A | Z004 igl Fab heavy chain | protein | 218 | 3% helix, 46% strand | S6C4S0 |
| C | Env | protein | 99 | 0% helix, 44% strand | A0A1X9PPI0 |
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 | 491 | 0.64 | 0.77 | 63 | empty |
| 2 | 545 | 0.59 | 0.73 | 62 | empty |
| 3 | 434 | 0.57 | 0.74 | 54 | empty |
| 4 | 142 | 0.44 | 0.76 | 25 | empty |
| 5 | 149 | 0.42 | 0.75 | 34 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1868 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1858 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 8 hydrogen bonds · protein-protein
- H–E · 447 Ų buried · 6 hydrogen bonds · protein-protein
- L–E · 292 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6UTA · Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII · the same entry in another collection · chain E against E, TM-score 1.00
- P0DOX7 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa light chain (P0DOX7) · a predicted model of the same protein · chain L against A, TM-score 0.97
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 S6C4S0
- Every structure of UniProt P0DOX7
- Every structure of UniProt A0A1X9PPI0
- Elsewhere: RCSB PDB 6UTA · PDBe 6UTA · UniProt S6C4S0 · UniProt P0DOX7 · UniProt A0A1X9PPI0
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