MolNFT v1 · #110105 · protein
Structure of the yeast coat nucleoporin complex, space group C2
4XMM · Protein transport protein SEC13: “Structure of the yeast coat nucleoporin complex, space group C2”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #110105 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4XMM
- Type
- protein
- Length
- 3,454 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC13; Nucleoporin NUP145; Nucleoporin SEH1; Nucleoporin NUP85…
- EC
- 3.4.21.-
- UniProt
- Q04491, P49687, P53011, P46673, P35729, P52891
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC13 | protein | 274 | 2% helix, 49% strand | Q04491 |
| B | Nucleoporin NUP145 (EC 3.4.21.-) | protein | 511 | 65% helix, 4% strand | P49687 |
| C | Nucleoporin SEH1 | protein | 307 | 2% helix, 51% strand | P53011 |
| D | Nucleoporin NUP85 | protein | 620 | 68% helix, 3% strand | P46673 |
| E | Nucleoporin NUP120 | protein | 896 | 45% helix, 21% strand | P35729 |
| F | Nucleoporin NUP84 | protein | 419 | 65% helix, 1% strand | P52891 |
| H | Antibody 57 heavy chain | protein | 217 | 8% helix, 51% strand | — |
| L | Antibody 57 light chain | protein | 210 | 6% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.88 | 0.89 | 74 | empty |
| 2 | 980 | 0.83 | 0.84 | 76 | empty |
| 3 | 622 | 0.76 | 0.82 | 74 | empty |
| 4 | 691 | 0.74 | 0.80 | 63 | empty |
| 5 | 300 | 0.71 | 0.85 | 43 | empty |
Interfaces
10 interfaces between chains.
- C–D · 3220 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2140 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 2009 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 1678 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 274 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4XMM · Structure of the yeast coat nucleoporin complex, space group C2 · the same entry in another collection · chain L against L, TM-score 1.00
- P52891 · AlphaFold monomer V2.0 prediction for nucleoporin NUP84 (P52891) · a predicted model of the same protein · chain F against A, TM-score 0.99
- P53011 · AlphaFold monomer V2.0 prediction for nucleoporin SEH1 (P53011) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q04491 · AlphaFold monomer V2.0 prediction for protein transport protein SEC13 (Q04491) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P49687 · AlphaFold monomer V2.0 prediction for nucleoporin NUP145 (P49687) · 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 Q04491
- Every structure of UniProt P49687
- Every structure of UniProt P53011
- Every structure of UniProt P46673
- Every structure of UniProt P35729
- Every structure of UniProt P52891
- Elsewhere: RCSB PDB 4XMM · PDBe 4XMM · UniProt Q04491 · UniProt P49687 · UniProt P53011 · UniProt P46673 · UniProt P35729 · UniProt P52891
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