Research workbench

Structure of ATP-grasp ligase psnb complexed with minimal precursor

Analyse Structure of ATP-grasp ligase psnb complexed with minimal precursor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DRO
Type: protein
Length: 1,795 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-grasp domain-containing protein; PSNA214-38, precursor peptide
UniProt: A6G4D7, A6GH40
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 8 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-grasp domain-containing protein	protein	299	37% helix, 27% strand	A6G4D7
B	ATP-grasp domain-containing protein	protein	300	36% helix, 27% strand	A6G4D7
C	ATP-grasp domain-containing protein	protein	303	35% helix, 26% strand	A6G4D7
D	ATP-grasp domain-containing protein	protein	289	35% helix, 24% strand	A6G4D7
E	ATP-grasp domain-containing protein	protein	296	38% helix, 25% strand	A6G4D7
F	ATP-grasp domain-containing protein	protein	285	36% helix, 25% strand	A6G4D7
G, I, J	PSNA214-38, precursor peptide	protein	6	0% helix, 0% strand	A6GH40
H	PSNA214-38, precursor peptide	protein	5	0% helix, 0% strand	A6GH40

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	860	0.72	0.77	78	empty
2	639	0.66	0.76	71	empty
3	259	0.57	0.78	42	empty
4	200	0.55	0.79	32	empty
5	280	0.53	0.75	46	empty

Interfaces

13 interfaces between chains.

E–F · 2443 Å² buried · 47 hydrogen bonds · protein-protein
A–B · 2402 Å² buried · 54 hydrogen bonds · protein-protein
C–D · 2243 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 1251 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 1199 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

7DRO · Structure of ATP-grasp ligase PsnB complexed with minimal precursor · 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 A6G4D7
Every structure of UniProt A6GH40
Elsewhere: RCSB PDB 7DRO · PDBe 7DRO · UniProt A6G4D7 · UniProt A6GH40

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.