MolNFT v1 · #169081 · protein
NUP84-NUP133 (AA521-1157) from S. cerevisiae bound by vhh-SAN8 and vhh-SAN9
6X03 · Nucleoporin NUP84: “NUP84-NUP133 (AA521-1157) from S. cerevisiae bound by vhh-SAN8 and vhh-SAN9”. X-ray diffraction, 15 pockets (best druggability 0.76). MolNFT v1 #169081 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6X03
- Type
- protein
- Length
- 1,429 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin NUP84; Nucleoporin NUP133; Vhh-SAN8; Vhh-SAN9
- UniProt
- P52891, P36161
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoporin NUP84 | protein | 650 | 57% helix, 0% strand | P52891 |
| B | Nucleoporin NUP133 | protein | 602 | 65% helix, 1% strand | P36161 |
| C | Vhh-SAN8 | protein | 90 | 3% helix, 43% strand | — |
| D | Vhh-SAN9 | protein | 87 | 3% helix, 44% strand | — |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.76 | 0.80 | 105 | empty |
| 2 | 1179 | 0.73 | 0.77 | 130 | empty |
| 3 | 748 | 0.71 | 0.78 | 83 | empty |
| 4 | 442 | 0.71 | 0.82 | 67 | empty |
| 5 | 501 | 0.71 | 0.80 | 67 | empty |
Interfaces
3 interfaces between chains.
- A–B · 254 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 147 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6X03 · Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9 · the same entry in another collection · chain A against A, TM-score 1.00
- P52891 · AlphaFold monomer V2.0 prediction for nucleoporin NUP84 (P52891) · a predicted model of the same protein · chain A against A, TM-score 0.90
- P36161 · AlphaFold monomer V2.0 prediction for nucleoporin NUP133 (P36161) · 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 P52891
- Every structure of UniProt P36161
- Elsewhere: RCSB PDB 6X03 · PDBe 6X03 · UniProt P52891 · UniProt P36161
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