Research workbench
Crystal structure of a clc-type FLUORIDE/PROTON antiporter
Analyse Crystal structure of a clc-type FLUORIDE/PROTON antiporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D0J
- Type
- protein
- Length
- 967 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clc-type FLUORIDE/PROTON antiporter; Monobody
- UniProt
- C9CPP6
- Ligands
- MHA, F
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clc-type FLUORIDE/PROTON antiporter | protein | 395 | 73% helix, 2% strand | C9CPP6 |
| B | Clc-type FLUORIDE/PROTON antiporter | protein | 396 | 72% helix, 2% strand | C9CPP6 |
| D | Monobody | protein | 86 | 0% helix, 49% strand | — |
| C | Monobody | protein | 90 | 0% helix, 50% strand | — |
Ligands and binding sites
- MHA · (carbamoylmethyl-carboxymethyl-amino)-acetic acid · ligand · chains C
- F · Fluoride ion · ion · 4 copies · chains A, B
- DMU · Decyl-beta-D-maltopyranoside · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.71 | 0.80 | 64 | empty |
| 2 | 363 | 0.70 | 0.82 | 41 | F |
| 3 | 337 | 0.70 | 0.83 | 33 | F |
| 4 | 537 | 0.68 | 0.78 | 65 | MHA |
| 5 | 323 | 0.60 | 0.77 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1596 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 850 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 848 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6D0J · Crystal structure of a CLC-type fluoride/proton antiporter · the same entry in another collection · chain A 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 C9CPP6
- Elsewhere: RCSB PDB 6D0J · PDBe 6D0J · UniProt C9CPP6
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