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Structural basis for adenylate kinase activity in ABC atpases

Analyse Structural basis for adenylate kinase activity in ABC atpases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KTA
Type: protein
Length: 656 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromosome segregation protein smc
UniProt: Q8TZY2
Ligands: AP5, MG
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chromosome segregation protein smc	protein	164	29% helix, 28% strand	Q8TZY2
B	Chromosome segregation protein smc	protein	171	46% helix, 21% strand	Q8TZY2
C	Chromosome segregation protein smc	protein	163	26% helix, 28% strand	Q8TZY2
D	Chromosome segregation protein smc	protein	158	49% helix, 23% strand	Q8TZY2

Ligands and binding sites

AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 2 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	433	0.71	0.82	63	empty
2	218	0.55	0.78	35	empty
3	112	0.40	0.76	20	empty
4	54	0.35	0.79	13	empty
5	55	0.32	0.76	13	empty

Interfaces

3 interfaces between chains.

A–B · 2832 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 2728 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 693 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

3KTA · Structural Basis for Adenylate Kinase Activity in ABC ATPases · the same entry in another collection · chain D against D, TM-score 1.00
Q8TZY2 · AlphaFold monomer V2.0 prediction for chromosome partition protein smc (Q8TZY2) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q8TZY2
Elsewhere: RCSB PDB 3KTA · PDBe 3KTA · UniProt Q8TZY2

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