MolNFT v1 · #113935 · protein

Precise resting state of thermus thermophilus secyeg

5AWW · Protein translocase subunit secy: “Precise resting state of thermus thermophilus secyeg”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #113935 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AWW
Type: protein
Length: 559 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein translocase subunit secy; Protein translocase subunit sece; Putative preprotein…
UniProt: Q5SHQ8, P38383, Q5SHE6
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Y	Protein translocase subunit secy	protein	424	72% helix, 6% strand	Q5SHQ8
E	Protein translocase subunit sece	protein	60	87% helix, 2% strand	P38383
G	Putative preprotein translocase, secg subunit	protein	75	61% helix, 0% strand	Q5SHE6

Ligands and binding sites

OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 11 copies · chains Y, E, G

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	735	0.79	0.82	71	empty
2	253	0.60	0.80	42	empty
3	340	0.58	0.76	43	empty
4	55	0.56	0.88	15	empty
5	60	0.55	0.88	16	empty

Interfaces

2 interfaces between chains.

Y–E · 1955 Å² buried · 14 hydrogen bonds · protein-protein
Y–G · 1943 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5AWW · Precise Resting State of Thermus thermophilus SecYEG · the same entry in another collection · chain Y against Y, TM-score 1.00
Q5SHQ8 · AlphaFold monomer V2.0 prediction for protein translocase subunit secy (Q5SHQ8) · a predicted model of the same protein · chain Y against A, TM-score 0.97
P38383 · AlphaFold monomer V2.0 prediction for protein translocase subunit sece (P38383) · a predicted model of the same protein · chain E against A, TM-score 0.73

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 Q5SHQ8
Every structure of UniProt P38383
Every structure of UniProt Q5SHE6
Elsewhere: RCSB PDB 5AWW · PDBe 5AWW · UniProt Q5SHQ8 · UniProt P38383 · UniProt Q5SHE6

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