Research workbench
Crystal structure of NUP358/RANBP2 ran-binding domain 3 in complex with ran-gppnhp
Analyse Crystal structure of NUP358/RANBP2 ran-binding domain 3 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
- 7MNY
- Type
- protein
- Length
- 2,004 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 0.85
Structure
x-ray diffraction · 11 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 208 | 31% helix, 23% strand | P62826 |
| B | E3 sumo-protein ligase RANBP2 (EC 2.3.2.-) | protein | 129 | 13% helix, 47% strand | P49792 |
| C | GTP-binding nuclear protein ran | protein | 202 | 33% helix, 24% strand | P62826 |
| D | E3 sumo-protein ligase RANBP2 (EC 2.3.2.-) | protein | 135 | 12% helix, 47% strand | P49792 |
| E | GTP-binding nuclear protein ran | protein | 203 | 31% helix, 24% strand | P62826 |
| F | E3 sumo-protein ligase RANBP2 (EC 2.3.2.-) | protein | 123 | 13% helix, 49% strand | P49792 |
| G | GTP-binding nuclear protein ran | protein | 205 | 32% helix, 23% strand | P62826 |
| H | E3 sumo-protein ligase RANBP2 (EC 2.3.2.-) | protein | 134 | 13% helix, 48% strand | P49792 |
| I | GTP-binding nuclear protein ran | protein | 203 | 30% helix, 24% strand | P62826 |
| J, L | E3 sumo-protein ligase RANBP2 (EC 2.3.2.-) | protein | 128 | 13% helix, 47% strand | P49792 |
| K | GTP-binding nuclear protein ran | protein | 206 | 33% helix, 23% 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.85 | 0.88 | 96 | GNP, MG |
| 2 | 479 | 0.82 | 0.89 | 83 | empty |
| 3 | 472 | 0.81 | 0.88 | 65 | GNP, MG |
| 4 | 289 | 0.79 | 0.90 | 52 | GNP, MG |
| 5 | 231 | 0.75 | 0.89 | 33 | empty |
Interfaces
23 interfaces between chains.
- C–D · 2526 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2473 Ų buried · 41 hydrogen bonds · protein-protein
- K–L · 2339 Ų buried · 41 hydrogen bonds · protein-protein
- I–J · 2294 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2251 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7MNY · Crystal Structure of Nup358/RanBP2 Ran-binding domain 3 in complex with Ran-GPPNHP · 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 P62826
- Every structure of UniProt P49792
- Elsewhere: RCSB PDB 7MNY · PDBe 7MNY · UniProt P62826 · UniProt P49792
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