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Thermus phage P74-26 large terminase ATPase domain bound to ADP beryllium fluoride

Analyse Thermus phage P74-26 large terminase ATPase domain bound to ADP beryllium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZNL
Type: protein
Length: 758 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phage terminase large subunit
UniProt: A7XXR1
Ligands: BEF, ADP, MG, SO4
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phage terminase large subunit	protein	253	40% helix, 21% strand	A7XXR1
B	Phage terminase large subunit	protein	254	38% helix, 22% strand	A7XXR1
C	Phage terminase large subunit	protein	251	39% helix, 21% strand	A7XXR1

Ligands and binding sites

BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, B, C
ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 3 copies · chains A, C, B

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

Pockets

7 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	1157	0.76	0.79	97	SO4, MG, BEF, ADP
2	443	0.68	0.80	63	empty
3	248	0.56	0.78	25	SO4
4	122	0.52	0.82	19	empty
5	92	0.39	0.76	21	empty

Interfaces

3 interfaces between chains.

B–C · 696 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 683 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 298 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4ZNL · Thermus Phage P74-26 Large Terminase ATPase domain bound to ADP Beryllium Fluoride · 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 A7XXR1
Elsewhere: RCSB PDB 4ZNL · PDBe 4ZNL · UniProt A7XXR1

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