Research workbench
Structure of norc transporter (K398A mutant) in an outward-open conformation in complex with a single-chain indian camelid antibody
Analyse Structure of norc transporter (K398A mutant) in an outward-open conformation in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D5Q
- Type
- protein
- Length
- 1,076 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Drug transporter, putative; Icab
- UniProt
- A0A0H2WZS4
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Drug transporter, putative | protein | 403 | 81% helix, 0% strand | A0A0H2WZS4 |
| B | Drug transporter, putative | protein | 411 | 80% helix, 0% strand | A0A0H2WZS4 |
| C, D | Icab | protein | 131 | 2% helix, 50% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.82 | 0.83 | 91 | empty |
| 2 | 1111 | 0.82 | 0.83 | 91 | empty |
| 3 | 329 | 0.56 | 0.75 | 34 | empty |
| 4 | 258 | 0.50 | 0.73 | 32 | empty |
| 5 | 70 | 0.46 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1319 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1304 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 399 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7D5Q · Structure of NorC transporter (K398A mutant) in an outward-open conformation in complex… · 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 A0A0H2WZS4
- Elsewhere: RCSB PDB 7D5Q · PDBe 7D5Q · UniProt A0A0H2WZS4
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