MolNFT v1 · #46716 · protein
Complex of the guanine exchange factor SEC2P and the rab GTPase SEC4P
2OCY · Rab guanine nucleotide exchange factor SEC2: “Complex of the guanine exchange factor SEC2P and the rab GTPase SEC4P”. X-ray diffraction, 3 pockets (best druggability 0.32). MolNFT v1 #46716 on GenesisL1: 3D structure, binding sites…
- PDB
- 2OCY
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rab guanine nucleotide exchange factor SEC2; RAS-related protein SEC4
- UniProt
- P17065, P07560
- Pockets
- 3 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rab guanine nucleotide exchange factor SEC2 | protein | 149 | 91% helix, 0% strand | P17065 |
| C | RAS-related protein SEC4 | protein | 147 | 33% helix, 16% strand | P07560 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.32 | 0.76 | 12 | empty |
| 2 | 56 | 0.31 | 0.76 | 15 | empty |
| 3 | 59 | 0.26 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3843 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 683 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 508 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2OCY · Complex of the guanine exchange factor Sec2p and the Rab GTPase Sec4p · the same entry in another collection · chain A against A, TM-score 1.00
- P07560 · AlphaFold monomer V2.0 prediction for RAS-related protein SEC4 (P07560) · a predicted model of the same protein · chain C against A, TM-score 0.84
- P17065 · AlphaFold monomer V2.0 prediction for rab guanine nucleotide exchange factor SEC2 (P17065) · a predicted model of the same protein · chain A against A, TM-score 0.54
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 P17065
- Every structure of UniProt P07560
- Elsewhere: RCSB PDB 2OCY · PDBe 2OCY · UniProt P17065 · UniProt P07560
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