Research workbench
Structure of the metazoan NUP62.NUP58.NUP54 nucleoporin complex.
Analyse Structure of the metazoan NUP62.NUP58.NUP54 nucleoporin complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C3L
- Type
- protein
- Length
- 506 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NUP54; Nucleoporin NUP58; Nucleoporin NUP62; Nanobody NB15; Part of NUP54 N-terminus with…
- UniProt
- K9ZTJ6, Q5EAX5, Q91349
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 66% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NUP54 | protein | 134 | 70% helix, 0% strand | K9ZTJ6 |
| B | Nucleoporin NUP58 | protein | 124 | 89% helix, 0% strand | Q5EAX5 |
| C | Nucleoporin NUP62 | protein | 122 | 93% helix, 0% strand | Q91349 |
| D | Nanobody NB15 | protein | 112 | 8% helix, 49% strand | — |
| H | Part of NUP54 N-terminus with weak electron density, built as poly-alanine. | protein | 14 | 50% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.66 | 0.78 | 44 | empty |
| 2 | 510 | 0.64 | 0.76 | 50 | empty |
| 3 | 77 | 0.41 | 0.79 | 14 | empty |
Interfaces
8 interfaces between chains.
- A–C · 2948 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2235 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1901 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 597 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 359 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5C3L · Structure of the metazoan Nup62.Nup58.Nup54 nucleoporin complex. · 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 K9ZTJ6
- Every structure of UniProt Q5EAX5
- Every structure of UniProt Q91349
- Elsewhere: RCSB PDB 5C3L · PDBe 5C3L · UniProt K9ZTJ6 · UniProt Q5EAX5 · UniProt Q91349
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