Research workbench
Complex of nucleoporin-98 and nanobody MS98-27 solved at 1.85A resolution
Analyse Complex of nucleoporin-98 and nanobody MS98-27 solved at 1.85A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NQA
- Type
- protein
- Length
- 552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear pore complex protein NUP96; Anti-NUP98 nanobody MS98-6
- UniProt
- F6ZMG3
- Ligands
- NA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear pore complex protein NUP96 | protein | 152 | 21% helix, 34% strand | F6ZMG3 |
| D, C | Anti-NUP98 nanobody MS98-6 | protein | 124 | 2% helix, 56% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, D, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.69 | 0.80 | 53 | TRS |
| 2 | 314 | 0.58 | 0.77 | 45 | empty |
| 3 | 108 | 0.41 | 0.76 | 19 | empty |
| 4 | 83 | 0.40 | 0.78 | 14 | empty |
| 5 | 99 | 0.37 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1019 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1001 Ų buried · 18 hydrogen bonds · protein-protein
- D–B · 427 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 6 hydrogen bonds · protein-protein
- D–C · 391 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7NQA · Crystal structure of Nucleoporin-98 nanobody MS98-6 complex solved at 2.2A resolution · 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 F6ZMG3
- Elsewhere: RCSB PDB 7NQA · PDBe 7NQA · UniProt F6ZMG3
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