Research workbench
Crystal structure of disulfide cross-linked D417C ClC-ec1
Analyse Crystal structure of disulfide cross-linked D417C ClC-ec1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HD8
- Type
- protein
- Length
- 1,728 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.15
- Source
- Escherichia coli; Mus musculus
- Molecule
- H(+)/Cl(-) exchange transporter ClcA; Fab fragment (heavy chain); Fab fragment (light…
- UniProt
- P37019
- Ligands
- CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 3.15 · 5 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H(+)/Cl(-) exchange transporter ClcA | protein | 433 | 79% helix, 0% strand | P37019 |
| B | H(+)/Cl(-) exchange transporter ClcA | protein | 432 | 77% helix, 0% strand | P37019 |
| C | Fab fragment (heavy chain) | protein | 221 | 5% helix, 50% strand | — |
| D, F | Fab fragment (light chain) | protein | 211 | 4% helix, 52% strand | — |
| E | Fab fragment (heavy chain) | protein | 220 | 4% helix, 53% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.77 | 0.88 | 34 | empty |
| 2 | 279 | 0.76 | 0.88 | 31 | empty |
| 3 | 287 | 0.69 | 0.84 | 27 | CL |
| 4 | 333 | 0.63 | 0.79 | 28 | CL |
| 5 | 595 | 0.63 | 0.75 | 59 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3509 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1958 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1936 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 511 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5HD8 · Crystal structure of disulfide cross-linked D417C clc-EC1 · the same entry in another collection · chain F against F, TM-score 1.00
- P37019 · AlphaFold monomer V2.0 prediction for H(+)/CL(-) exchange transporter clca (P37019) · a predicted model of the same protein · chain B against A, 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 P37019
- Elsewhere: RCSB PDB 5HD8 · PDBe 5HD8 · UniProt P37019
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