MolNFT v1 · #85215 · protein

Redox regulator hypr in its oxidized form

4A5M · Uncharacterized hth-type transcriptional regulator yybr: “Redox regulator hypr in its oxidized form”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.72). MolNFT v1 #85215 on GenesisL1: 3D structure, binding sites…

PDB: 4A5M
Type: protein
Length: 772 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized hth-type transcriptional regulator yybr
UniProt: P37486
Ligands: CL
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Uncharacterized hth-type transcriptional regulator yybr	protein	96	57% helix, 15% strand	P37486
B, D, F, H	Uncharacterized hth-type transcriptional regulator yybr	protein	97	57% helix, 14% strand	P37486

Ligands and binding sites

CL · Chloride ion · ion · chains E, F
EDO · 1,2-ethanediol · additive · 9 copies · chains A, E, H, D

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	743	0.72	0.78	63	empty
2	559	0.63	0.75	56	empty
3	366	0.59	0.76	33	EDO
4	243	0.55	0.77	35	EDO
5	237	0.46	0.73	29	empty

Interfaces

14 interfaces between chains.

E–F · 1478 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1473 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1452 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 1339 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 652 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4A5M · Redox regulator HypR in its oxidized form · the same entry in another collection · chain H against H, TM-score 1.00
P37486 · AlphaFold monomer V2.0 prediction for uncharacterized hth-type transcriptional regulator… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P37486
Elsewhere: RCSB PDB 4A5M · PDBe 4A5M · UniProt P37486

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