MolNFT v1 · #150436 · protein

Crystal structure of smba in complex with ppgpp.

6GTM: “Crystal structure of smba in complex with ppgpp.”. X-ray diffraction, 1 ligand (G4P), 9 pockets (best druggability 0.63). MolNFT v1 #150436 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GTM
Type: protein
Length: 1,152 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Smba
UniProt: Q9A5E6
Ligands: G4P
Pockets: 9 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Smba	protein	288	41% helix, 17% strand	Q9A5E6

Ligands and binding sites

G4P · Guanosine-5',3'-tetraphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	385	0.63	0.78	42	empty
2	152	0.44	0.75	22	empty
3	132	0.42	0.75	23	empty
4	153	0.40	0.73	17	empty
5	88	0.39	0.77	11	empty

Interfaces

3 interfaces between chains.

C–D · 395 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 316 Å² buried · 1 hydrogen bond · protein-protein
A–D · 223 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6GTM · Crystal structure of SmbA in complex with ppGpp. · 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 Q9A5E6
Elsewhere: RCSB PDB 6GTM · PDBe 6GTM · UniProt Q9A5E6

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