Research workbench
Structure of multidrug and toxin compound extrusion (mate) transporter norm by nabfab-fiducial assisted cryo-EM
Analyse Structure of multidrug and toxin compound extrusion (mate) transporter norm by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PHP
- Type
- protein
- Length
- 1,134 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug resistance protein norm; Nabfab hc; Nabfab lc; Norm-NB17_4; Anti-Fab nanobody
- UniProt
- D7H904
- Pockets
- 9 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug resistance protein norm | protein | 456 | 78% helix, 0% strand | D7H904 |
| H | Nabfab hc | protein | 228 | 8% helix, 44% strand | — |
| L | Nabfab lc | protein | 208 | 6% helix, 48% strand | — |
| N | Norm-NB17_4 | protein | 122 | 2% helix, 40% strand | — |
| K | Anti-Fab nanobody | protein | 120 | 5% helix, 43% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.85 | 0.86 | 91 | empty |
| 2 | 53 | 0.68 | 0.97 | 15 | empty |
| 3 | 110 | 0.65 | 0.89 | 30 | empty |
| 4 | 209 | 0.46 | 0.74 | 45 | empty |
| 5 | 76 | 0.37 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1912 Ų buried · 13 hydrogen bonds · protein-protein
- A–N · 900 Ų buried · 4 hydrogen bonds · protein-protein
- H–N · 768 Ų buried · 6 hydrogen bonds · protein-protein
- L–K · 717 Ų buried · 5 hydrogen bonds · protein-protein
- L–N · 279 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7PHP · Structure of Multidrug and Toxin Compound Extrusion (MATE) transporter NorM by… · 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 D7H904
- Elsewhere: RCSB PDB 7PHP · PDBe 7PHP · UniProt D7H904
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