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Crystal structure of full length tylp, a tetr regulator from streptomyces fradiae

Analyse Crystal structure of full length tylp, a tetr regulator from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XAY
Type: protein
Length: 1,649 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gamma-butyrolactone receptor protein
UniProt: Q9XCC7
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 7 distinct chains · 71% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gamma-butyrolactone receptor protein	protein	215	73% helix, 2% strand	Q9XCC7
B, G	Gamma-butyrolactone receptor protein	protein	215	70% helix, 2% strand	Q9XCC7
C	Gamma-butyrolactone receptor protein	protein	219	72% helix, 2% strand	Q9XCC7
D	Gamma-butyrolactone receptor protein	protein	197	72% helix, 1% strand	Q9XCC7
E	Gamma-butyrolactone receptor protein	protein	197	71% helix, 1% strand	Q9XCC7
F	Gamma-butyrolactone receptor protein	protein	199	71% helix, 1% strand	Q9XCC7
H	Gamma-butyrolactone receptor protein	protein	192	70% helix, 1% strand	Q9XCC7

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	218	0.78	0.91	40	empty
2	211	0.77	0.91	36	empty
3	180	0.77	0.92	33	empty
4	202	0.77	0.91	41	empty
5	958	0.76	0.79	95	empty

Interfaces

13 interfaces between chains.

C–E · 1548 Å² buried · 8 hydrogen bonds · protein-protein
D–G · 1535 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 1530 Å² buried · 7 hydrogen bonds · protein-protein
A–H · 1510 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 463 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 modified (engineered).

Compared structures

5XAY · Crystal structure of full length tylp, a tetr regulator from streptomyces fradiae · 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 Q9XCC7
Elsewhere: RCSB PDB 5XAY · PDBe 5XAY · UniProt Q9XCC7

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