Research workbench
Crystal structure of NUP358/RANBP2 ran-binding domain 4 in complex with ran-gppnhp
Analyse Crystal structure of NUP358/RANBP2 ran-binding domain 4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MNZ
- Type
- protein
- Length
- 2,060 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; E3 sumo-protein ligase RANBP2
- EC
- 2.3.2.-
- UniProt
- P62826, P49792
- Ligands
- GNP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | GTP-binding nuclear protein ran | protein | 206 | 30% helix, 24% strand | P62826 |
| B, D, F, H, J, L | E3 sumo-protein ligase RANBP2 (EC 2.3.2.-) | protein | 138 | 12% helix, 45% strand | P49792 |
| C, K | GTP-binding nuclear protein ran | protein | 205 | 31% helix, 22% strand | P62826 |
| I | GTP-binding nuclear protein ran | protein | 204 | 31% helix, 24% strand | P62826 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, C, E, G, I, K
- MG · Magnesium ion · metal · 6 copies · chains A, C, E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.78 | 0.81 | 103 | GNP, MG |
| 2 | 1090 | 0.76 | 0.79 | 92 | empty |
| 3 | 947 | 0.75 | 0.78 | 86 | empty |
| 4 | 504 | 0.75 | 0.83 | 57 | GNP, MG |
| 5 | 472 | 0.67 | 0.78 | 48 | empty |
Interfaces
33 interfaces between chains.
- E–F · 2563 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2534 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2496 Ų buried · 35 hydrogen bonds · protein-protein
- K–L · 2402 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2381 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7MNZ · Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP · the same entry in another collection · chain G against G, 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 P62826
- Every structure of UniProt P49792
- Elsewhere: RCSB PDB 7MNZ · PDBe 7MNZ · UniProt P62826 · UniProt P49792
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