Research workbench
Structure of human REP15:RAB3B_Q81L complex.
Analyse Structure of human REP15:RAB3B_Q81L complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8A4B
- Type
- protein
- Length
- 752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAB15 effector protein; RAS-related protein rab-3B
- UniProt
- Q6BDI9, P20337
- Ligands
- GTP, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAB15 effector protein | protein | 208 | 36% helix, 20% strand | Q6BDI9 |
| B | RAS-related protein rab-3B | protein | 170 | 37% helix, 29% strand | P20337 |
| C | RAB15 effector protein | protein | 205 | 41% helix, 22% strand | Q6BDI9 |
| D | RAS-related protein rab-3B | protein | 169 | 37% helix, 29% strand | P20337 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.77 | 0.79 | 121 | GTP, MG |
| 2 | 84 | 0.74 | 0.96 | 31 | empty |
| 3 | 546 | 0.72 | 0.80 | 62 | GTP, MG |
| 4 | 191 | 0.53 | 0.78 | 24 | empty |
| 5 | 91 | 0.48 | 0.81 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1045 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 909 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 826 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 8A4B · Structure of human Rep15:Rab3B_Q81L complex. · the same entry in another collection · chain D against D, TM-score 1.00
- P20337 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-3B (P20337) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q6BDI9 · AlphaFold monomer V2.0 prediction for RAB15 effector protein (Q6BDI9) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q6BDI9
- Every structure of UniProt P20337
- Elsewhere: RCSB PDB 8A4B · PDBe 8A4B · UniProt Q6BDI9 · UniProt P20337
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