Research workbench
Model of complex between the E.COLI enzyme beta-galactosidase and four single chain fv antibody domains SCFV13R4.
Analyse Model of complex between the E.COLI enzyme beta-galactosidase and four single… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CKD
- Type
- protein
- Length
- 4,968 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase; SCFV13R4 antibody fv heavy chain; SCFV13R4 antibody fv light chain
- EC
- 3.2.1.23
- UniProt
- P00722
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1021 | 14% helix, 40% strand | P00722 |
| H, I, J, K | SCFV13R4 antibody fv heavy chain | protein | 114 | 8% helix, 51% strand | — |
| L, M, N, O | SCFV13R4 antibody fv light chain | protein | 107 | 3% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.85 | 0.86 | 118 | empty |
| 2 | 1195 | 0.85 | 0.86 | 122 | empty |
| 3 | 1182 | 0.85 | 0.86 | 123 | empty |
| 4 | 1200 | 0.83 | 0.84 | 106 | empty |
| 5 | 960 | 0.82 | 0.83 | 97 | empty |
Interfaces
18 interfaces between chains.
- B–C · 2402 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2368 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2023 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2017 Ų buried · 25 hydrogen bonds · protein-protein
- D–I · 826 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4CKD · Model of complex between the E.coli enzyme beta-galactosidase and four single chain Fv… · the same entry in another collection · chain O against O, 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 P00722
- Elsewhere: RCSB PDB 4CKD · PDBe 4CKD · UniProt P00722
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