Research workbench
Crystal structure of RAB9A-GTP-NDE1
Analyse Crystal structure of RAB9A-GTP-NDE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E1T
- Type
- protein
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-9A; Isoform 2 of nuclear distribution protein nude homolog 1
- UniProt
- P51151, Q9NXR1
- Ligands
- GTP, MG
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-9A | protein | 170 | 37% helix, 26% strand | P51151 |
| B | RAS-related protein rab-9A | protein | 174 | 36% helix, 25% strand | P51151 |
| C | Isoform 2 of nuclear distribution protein nude homolog 1 | protein | 33 | 94% helix, 0% strand | Q9NXR1 |
| D | Isoform 2 of nuclear distribution protein nude homolog 1 | protein | 25 | 92% helix, 0% strand | Q9NXR1 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.54 | 0.81 | 26 | MG, GTP |
| 2 | 134 | 0.50 | 0.80 | 28 | MG, GTP |
| 3 | 174 | 0.49 | 0.77 | 24 | empty |
| 4 | 185 | 0.48 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 574 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 484 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 470 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 309 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7E1T · Crystal structure of Rab9A-GTP-Nde1 · the same entry in another collection · chain D against D, TM-score 1.00
- P51151 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-9A (P51151) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9NXR1 · AlphaFold monomer V2.0 prediction for nuclear distribution protein nude homolog 1 (Q9NXR1) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P51151
- Every structure of UniProt Q9NXR1
- Elsewhere: RCSB PDB 7E1T · PDBe 7E1T · UniProt P51151 · UniProt Q9NXR1
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