MolNFT v1 · #169086 · protein
NUP85-SEH1 from S. cerevisiae bound by vhh-SAN2
6X08 · Nucleoporin SEH1: “NUP85-SEH1 from S. cerevisiae bound by vhh-SAN2”. X-ray diffraction, 12 pockets (best druggability 0.87). MolNFT v1 #169086 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6X08
- Type
- protein
- Length
- 910 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin SEH1; Nucleoporin NUP85; Vhh-SAN2
- UniProt
- P53011, P46673
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoporin SEH1 | protein | 310 | 2% helix, 49% strand | P53011 |
| B | Nucleoporin NUP85 | protein | 475 | 60% helix, 3% strand | P46673 |
| K | Vhh-SAN2 | protein | 125 | 2% helix, 37% strand | — |
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.87 | 0.89 | 75 | empty |
| 2 | 563 | 0.75 | 0.82 | 72 | empty |
| 3 | 247 | 0.69 | 0.84 | 39 | empty |
| 4 | 164 | 0.65 | 0.86 | 41 | empty |
| 5 | 499 | 0.64 | 0.76 | 59 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3119 Ų buried · 23 hydrogen bonds · protein-protein
- B–K · 395 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6X08 · Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2 · the same entry in another collection · chain A against A, TM-score 1.00
- P53011 · AlphaFold monomer V2.0 prediction for nucleoporin SEH1 (P53011) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P46673 · AlphaFold monomer V2.0 prediction for nucleoporin NUP85 (P46673) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P53011
- Every structure of UniProt P46673
- Elsewhere: RCSB PDB 6X08 · PDBe 6X08 · UniProt P53011 · UniProt P46673
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