MolNFT v1 · #139275 · protein

Crystal structure of secdf in I form (C2 space group)

5XAP · Protein translocase subunit secd: “Crystal structure of secdf in I form (C2 space group)”. X-ray diffraction, 10 pockets (best druggability 0.83). MolNFT v1 #139275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XAP
Type: protein
Length: 732 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein translocase subunit secd
UniProt: Q9RTE3
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 60% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein translocase subunit secd	protein	732	60% helix, 15% strand	Q9RTE3

Ligands and binding sites

OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 7 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	831	0.83	0.85	86	empty
2	298	0.65	0.80	28	OLC
3	90	0.56	0.86	17	empty
4	149	0.54	0.81	30	PEG
5	192	0.50	0.76	28	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5XAP · Crystal structure of SecDF in I form (C2 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 5XAP · PDBe 5XAP · UniProt Q9RTE3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.