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Structure of ATP-grasp ligase psnb complexed with minimal precursor, mg, and ADP

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

PDB: 7DRM
Type: protein
Length: 1,260 residues
Chains: 6
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
Ligands: ADP, MG
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-grasp domain-containing protein	protein	311	38% helix, 24% strand	A6G4D7
B	ATP-grasp domain-containing protein	protein	295	39% helix, 24% strand	A6G4D7
C	ATP-grasp domain-containing protein	protein	311	39% helix, 24% strand	A6G4D7
D	ATP-grasp domain-containing protein	protein	309	38% helix, 23% strand	A6G4D7
E	PSNA214-38, precursor peptide	protein	18	17% helix, 0% strand	A6GH40
F	PSNA214-38, precursor peptide	protein	16	0% helix, 0% strand	A6GH40

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, E, C
MG · Magnesium ion · metal · 4 copies · chains A, E, C, F

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1111	0.80	0.82	89	ADP, MG
2	1145	0.79	0.80	89	ADP, MG
3	1043	0.78	0.80	114	empty
4	145	0.51	0.79	28	empty
5	88	0.47	0.81	23	empty

Interfaces

10 interfaces between chains.

C–D · 2537 Å² buried · 48 hydrogen bonds · protein-protein
A–B · 2431 Å² buried · 43 hydrogen bonds · protein-protein
C–F · 857 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 852 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 623 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7DRM · Structure of ATP-grasp ligase PsnB complexed with minimal precursor, Mg, and ADP · the same entry in another collection · chain E against E, 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 7DRM · PDBe 7DRM · UniProt A6G4D7 · UniProt A6GH40

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