Research workbench
Structure of human clc-7/OSTM1 complex
Analyse Structure of human clc-7/OSTM1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JM7
- Type
- protein
- Length
- 1,802 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Osteopetrosis-associated transmembrane protein 1; H(+)/CL(-) exchange transporter 7
- UniProt
- Q86WC4, P51798
- Ligands
- ATP, 0J1, NAG, MAN, BMA, MG, CL
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 62% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Osteopetrosis-associated transmembrane protein 1 | protein | 218 | 73% helix, 2% strand | Q86WC4 |
| A, C | H(+)/CL(-) exchange transporter 7 | protein | 683 | 59% helix, 8% strand | P51798 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- 0J1 · (2R)-3-{[(R)-hydroxy{[(1s,2r,3s,4s,5r,6r)-2,3,4,6-tetrahydroxy-5-(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dinonanoate · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains B, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains D, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains D, B
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1080 | 0.82 | 0.83 | 84 | empty |
| 2 | 678 | 0.80 | 0.85 | 43 | empty |
| 3 | 744 | 0.80 | 0.84 | 70 | 0J1 |
| 4 | 761 | 0.79 | 0.82 | 68 | 0J1 |
| 5 | 524 | 0.75 | 0.83 | 65 | empty |
Interfaces
4 interfaces between chains.
- A–C · 3114 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 2343 Ų buried · 23 hydrogen bonds · protein-protein
- D–C · 1227 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 1227 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7JM7 · Structure of human CLC-7/OSTM1 complex · the same entry in another collection · chain B against B, TM-score 1.00
- P51798 · AlphaFold monomer V2.0 prediction for H(+)/CL(-) exchange transporter 7 (P51798) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q86WC4 · AlphaFold monomer V2.0 prediction for osteopetrosis-associated transmembrane protein 1… · a predicted model of the same protein · chain B against A, TM-score 0.81
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 Q86WC4
- Every structure of UniProt P51798
- Elsewhere: RCSB PDB 7JM7 · PDBe 7JM7 · UniProt Q86WC4 · UniProt P51798
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