MolNFT v1 · #34426 · protein

Structure of shikimate kinase from mycobacterium tuberculosis complexed with ADP and mg at 2.8 angstrons of resolution

2DFT: “Structure of shikimate kinase from mycobacterium tuberculosis complexed with ADP and mg at 2.8 angstrons of…”. X-ray diffraction, 3 ligands (ADP, MG, CL), 8 pockets (best druggability 0.81). MolNFT v1 #34426 on GenesisL1: 3D…

PDB: 2DFT
Type: protein
Length: 641 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Shikimate kinase
EC: 2.7.1.71
UniProt: P0A4Z2
Ligands: ADP, MG, CL
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Shikimate kinase (EC 2.7.1.71)	protein	156	59% helix, 12% strand	P0A4Z2
B, D	Shikimate kinase (EC 2.7.1.71)	protein	165	53% helix, 12% strand	P0A4Z2
C	Shikimate kinase (EC 2.7.1.71)	protein	155	53% helix, 12% strand	P0A4Z2

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 3 copies · chains A, B, D

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	855	0.81	0.84	89	MG, ADP, CL
2	679	0.78	0.83	74	ADP, MG, CL
3	433	0.70	0.81	56	empty
4	166	0.59	0.83	29	MG, CL
5	203	0.57	0.80	27	empty

Interfaces

6 interfaces between chains.

A–C · 910 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 519 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 486 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 423 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 151 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2DFT · Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg… · 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 P0A4Z2
Elsewhere: RCSB PDB 2DFT · PDBe 2DFT · UniProt P0A4Z2

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