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Crystal structure of the N-terminal domain of NUP358/RANBP2 (residues 1-752) T585M mutant in complex with Fab fragment
Analyse Crystal structure of the N-terminal domain of NUP358/RANBP2 (residues 1-752)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MNM
- Type
- protein
- Length
- 2,228 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 sumo-protein ligase RANBP2; Antibody FAB14 heavy chain; Antibody FAB14 light chain
- EC
- 2.3.2.-
- UniProt
- P49792
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 13% 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 | 602 | 71% helix, 0% strand | P49792 |
| H, K | Antibody FAB14 heavy chain | protein | 227 | 7% helix, 52% strand | — |
| L, M | Antibody FAB14 light chain | protein | 213 | 6% helix, 53% strand | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.81 | 0.85 | 61 | empty |
| 2 | 1015 | 0.73 | 0.76 | 95 | empty |
| 3 | 695 | 0.72 | 0.79 | 86 | empty |
| 4 | 506 | 0.65 | 0.77 | 56 | empty |
| 5 | 508 | 0.65 | 0.77 | 52 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1989 Ų buried · 16 hydrogen bonds · protein-protein
- K–M · 1938 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1073 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 989 Ų buried · 14 hydrogen bonds · protein-protein
- B–K · 823 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7MNM · Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) T585M mutant… · 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 7MNM · PDBe 7MNM · UniProt P49792
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