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Structure of S. venezuelae risg-whig-C-di-gmp complex: orthorhombic crystal form

Analyse Structure of S. venezuelae risg-whig-C-di-gmp complex: orthorhombic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PFV
Type: protein
Length: 1,146 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amfc protein; RNA polymerase sigma factor
UniProt: F2RFR7, A0A3N1Q704
Ligands: C2E
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	Amfc protein	protein	164	70% helix, 0% strand	F2RFR7
A, D	RNA polymerase sigma factor	protein	220	70% helix, 0% strand	A0A3N1Q704
B	Amfc protein	protein	160	68% helix, 0% strand	F2RFR7
E	Amfc protein	protein	159	70% helix, 0% strand	F2RFR7
G	RNA polymerase sigma factor	protein	223	70% helix, 0% strand	A0A3N1Q704

Ligands and binding sites

C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 6 copies · chains T, A, B, D, E, G

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.79	0.82	98	C2E
2	1050	0.76	0.79	87	C2E
3	761	0.70	0.77	62	C2E
4	58	0.62	0.92	17	empty
5	106	0.61	0.87	18	empty

Interfaces

7 interfaces between chains.

E–G · 2486 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 2453 Å² buried · 26 hydrogen bonds · protein-protein
T–A · 2416 Å² buried · 35 hydrogen bonds · protein-protein
T–D · 947 Å² buried · 11 hydrogen bonds · protein-protein
T–G · 328 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6PFV · Structure of S. venezuelae RisG-WhiG-c-di-GMP complex: orthorhombic crystal form · the same entry in another collection · chain T against T, 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 F2RFR7
Every structure of UniProt A0A3N1Q704
Elsewhere: RCSB PDB 6PFV · PDBe 6PFV · UniProt F2RFR7 · UniProt A0A3N1Q704

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