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Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) in complex with Fab fragment
Analyse Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MNL
- Type
- protein
- Length
- 2,219 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.95
- Source
- Homo sapiens
- Molecule
- E3 SUMO-protein ligase RanBP2; Antibody Fab14 Heavy Chain; Antibody Fab14 Light Chain
- EC
- 2.3.2.-
- UniProt
- P49792
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 3.95 · 5 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 SUMO-protein ligase RanBP2 (EC 2.3.2.-) | protein | 746 | 73% helix, 0% strand | P49792 |
| B | E3 SUMO-protein ligase RanBP2 (EC 2.3.2.-) | protein | 594 | 72% helix, 0% strand | P49792 |
| H, K | Antibody Fab14 Heavy Chain | protein | 227 | 8% helix, 52% strand | — |
| L | Antibody Fab14 Light Chain | protein | 213 | 6% helix, 52% strand | — |
| M | Antibody Fab14 Light Chain | protein | 212 | 6% helix, 53% strand | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.80 | 0.82 | 71 | empty |
| 2 | 1004 | 0.72 | 0.76 | 93 | empty |
| 3 | 569 | 0.67 | 0.77 | 62 | empty |
| 4 | 390 | 0.65 | 0.79 | 45 | empty |
| 5 | 446 | 0.63 | 0.77 | 46 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1986 Ų buried · 15 hydrogen bonds · protein-protein
- K–M · 1899 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1028 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 997 Ų buried · 13 hydrogen bonds · protein-protein
- B–K · 831 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7MNL · Crystal structure of the N-terminal domain of NUP358/RANBP2 (residues 1-752) in 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 P49792
- Elsewhere: RCSB PDB 7MNL · PDBe 7MNL · UniProt P49792
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