MolNFT v1 · #28411 · protein

Crystal structure of TRP repressor binding protein wrba

1YDG: “Crystal structure of TRP repressor binding protein wrba”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.73). MolNFT v1 #28411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YDG
Type: protein
Length: 1,616 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRP repressor binding protein wrba
UniProt: Q9RYU4
Ligands: SO4
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	TRP repressor binding protein wrba	protein	201	43% helix, 18% strand	Q9RYU4
B, C, D, G, H	TRP repressor binding protein wrba	protein	202	46% helix, 18% strand	Q9RYU4
E	TRP repressor binding protein wrba	protein	204	44% helix, 18% strand	Q9RYU4

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	800	0.73	0.78	88	SO4
2	324	0.72	0.85	54	SO4
3	405	0.68	0.80	47	SO4
4	285	0.66	0.82	44	SO4
5	208	0.64	0.83	35	SO4

Interfaces

15 interfaces between chains.

C–D · 1270 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1244 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 1238 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1222 Å² buried · 11 hydrogen bonds · protein-protein
E–G · 877 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1YDG · Crystal Structure of Trp repressor binding protein WrbA · the same entry in another collection · chain H against H, TM-score 1.00
Q9RYU4 · AlphaFold monomer V2.0 prediction for NAD(P)H dehydrogenase (quinone) (Q9RYU4) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9RYU4
Elsewhere: RCSB PDB 1YDG · PDBe 1YDG · UniProt Q9RYU4

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