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Structure of ft (mgla-sspa)-ppgpp-pigr peptide complex

Analyse Structure of ft (mgla-sspa)-ppgpp-pigr peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WEG
Type: protein
Length: 812 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stringent starvation protein a, regulator of transcription; Mgla; Peptide
UniProt: Q5NHJ6, A0A0E2ZLH6, Q5NHR4
Ligands: G4P, MG
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 58% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Stringent starvation protein a, regulator of transcription	protein	193	58% helix, 7% strand	Q5NHJ6
A	Mgla	protein	204	59% helix, 6% strand	A0A0E2ZLH6
D	Stringent starvation protein a, regulator of transcription	protein	194	57% helix, 9% strand	Q5NHJ6
B	Mgla	protein	202	61% helix, 6% strand	A0A0E2ZLH6
P	Peptide	protein	19	37% helix, 0% strand	Q5NHR4

Ligands and binding sites

G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains C, A, D, B, P
MG · Magnesium ion · metal · 2 copies · chains C, D

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

Pockets

11 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	255	0.80	0.92	47	empty
2	513	0.76	0.84	65	empty
3	809	0.75	0.79	80	G4P
4	286	0.68	0.83	37	G4P
5	122	0.66	0.88	21	empty

Interfaces

6 interfaces between chains.

C–A · 991 Å² buried · 14 hydrogen bonds · protein-protein
D–B · 947 Å² buried · 15 hydrogen bonds · protein-protein
D–P · 631 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 617 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 541 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6WEG · Structure of Ft (MglA-SspA)-ppGpp-PigR peptide complex · the same entry in another collection · chain C against C, 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 Q5NHJ6
Every structure of UniProt A0A0E2ZLH6
Every structure of UniProt Q5NHR4
Elsewhere: RCSB PDB 6WEG · PDBe 6WEG · UniProt Q5NHJ6 · UniProt A0A0E2ZLH6 · UniProt Q5NHR4

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