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The crystal structure of a marr transcriptional regulator from methanosarcina mazei GO1

Analyse The crystal structure of a marr transcriptional regulator from methanosarcina… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S2W
Type: protein
Length: 1,109 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator, marr family
UniProt: Q8PVU7
Ligands: SO4
Pockets: 15 · best druggability 0.76

Structure

x-ray diffraction · 7 distinct chains · 70% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulator, marr family	protein	146	68% helix, 8% strand	Q8PVU7
B	Transcriptional regulator, marr family	protein	137	71% helix, 7% strand	Q8PVU7
C, D	Transcriptional regulator, marr family	protein	138	71% helix, 9% strand	Q8PVU7
E	Transcriptional regulator, marr family	protein	135	72% helix, 7% strand	Q8PVU7
F	Transcriptional regulator, marr family	protein	142	73% helix, 7% strand	Q8PVU7
G	Transcriptional regulator, marr family	protein	134	69% helix, 7% strand	Q8PVU7
H	Transcriptional regulator, marr family	protein	139	63% helix, 9% strand	Q8PVU7

Ligands and binding sites

SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E, F, H, G

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

Pockets

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	105	0.76	0.96	21	empty
2	114	0.75	0.95	27	empty
3	88	0.73	0.96	23	empty
4	77	0.72	0.96	20	empty
5	137	0.70	0.90	26	empty

Interfaces

9 interfaces between chains.

C–D · 2851 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 2848 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 2760 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 2688 Å² buried · 18 hydrogen bonds · protein-protein
F–H · 500 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 modified (engineered).

Compared structures

3S2W · The crystal structure of a MarR transcriptional regulator from Methanosarcina mazei Go1 · 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 Q8PVU7
Elsewhere: RCSB PDB 3S2W · PDBe 3S2W · UniProt Q8PVU7

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