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Crystal structure of mycobacterium tuberculosis C171Q kasa variant with bound tlm

Analyse Crystal structure of mycobacterium tuberculosis C171Q kasa variant with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WGG
Type: protein
Length: 3,320 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-oxoacyl-[acyl-carrier-protein] synthase 1
EC: 2.3.1.41
UniProt: P63454
Ligands: TLM, NA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	3-oxoacyl-[acyl-carrier-protein] synthase 1 (EC 2.3.1.41)	protein	415	39% helix, 20% strand	P63454

Ligands and binding sites

TLM · Thiolactomycin · ligand · 8 copies · chains A, B, C, D, E, F, G, H
NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
2PE · Nonaethylene glycol · additive · 8 copies · chains A, B, C, D, E, F, G, H
PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, D, C, F, G

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1022	0.83	0.84	103	TLM
2	860	0.83	0.85	86	TLM, PEG
3	409	0.80	0.88	44	2PE
4	405	0.80	0.88	43	2PE, PEG
5	393	0.79	0.88	41	PEG, 2PE

Interfaces

10 interfaces between chains.

G–H · 3339 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 3331 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 3322 Å² buried · 41 hydrogen bonds · protein-protein
E–F · 3208 Å² buried · 42 hydrogen bonds · protein-protein
D–E · 345 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2WGG · Crystal Structure of Mycobacterium tuberculosis C171Q KasA variant with bound TLM · 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 P63454
Elsewhere: RCSB PDB 2WGG · PDBe 2WGG · UniProt P63454

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