MolNFT v1 · #139273 · protein
Crystal structure of secdf in I form (P212121 space group)
5XAN · Protein translocase subunit secd: “Crystal structure of secdf in I form (P212121 space group)”. X-ray diffraction, 20 pockets (best druggability 0.89). MolNFT v1 #139273 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XAN
- Type
- protein
- Length
- 1,461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translocase subunit secd
- UniProt
- Q9RTE3
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein translocase subunit secd | protein | 728 | 59% helix, 15% strand | Q9RTE3 |
| B | Protein translocase subunit secd | protein | 733 | 60% helix, 15% strand | Q9RTE3 |
Ligands and binding sites
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 9 copies · chains A, B
- 15P · Polyethylene glycol (N=34) · additive · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.89 | 0.91 | 125 | 15P |
| 2 | 887 | 0.85 | 0.86 | 103 | empty |
| 3 | 417 | 0.64 | 0.77 | 40 | OLC |
| 4 | 280 | 0.63 | 0.80 | 26 | OLC |
| 5 | 512 | 0.62 | 0.75 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 532 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5XAN · Crystal structure of SecDF in I form (P212121 space group) · 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 Q9RTE3
- Elsewhere: RCSB PDB 5XAN · PDBe 5XAN · UniProt Q9RTE3
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