MolNFT v1 · #151944 · protein

Crystal structure of the mycobacterium tuberculosis pknb kinase domain (L33E mutant) in complex with its substrate gara

6I2P · SERINE/THREONINE-protein kinase pknb: “Crystal structure of the mycobacterium tuberculosis pknb kinase domain (L33E mutant) in complex with its…”. X-ray diffraction, 3 ligands (ACP, MG, SO4), 5 pockets (best druggability 0.82).…

PDB: 6I2P
Type: protein
Length: 761 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase pknb; Glycogen accumulation regulator gara…
EC: 2.7.11.1
UniProt: P9WI81, P9WJA9
Ligands: ACP, MG, SO4
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 5 distinct chains · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase pknb (EC 2.7.11.1)	protein	272	38% helix, 21% strand	P9WI81
B	SERINE/THREONINE-protein kinase pknb (EC 2.7.11.1)	protein	266	37% helix, 21% strand	P9WI81
D	Glycogen accumulation regulator gara	protein	114	3% helix, 43% strand	P9WJA9
E	Glycogen accumulation regulator gara	protein	104	0% helix, 46% strand	P9WJA9
C	Unk-unk-unk-unk-unk	protein	5	0% helix, 0% strand	—

Ligands and binding sites

ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, D

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

Pockets

5 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	1117	0.82	0.83	107	ACP, MG
2	623	0.78	0.84	79	ACP, MG
3	205	0.49	0.76	26	empty
4	138	0.46	0.77	23	SO4
5	83	0.40	0.78	16	empty

Interfaces

5 interfaces between chains.

A–D · 1125 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 654 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 559 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 215 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 114 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

6I2P · Crystal structure of the Mycobacterium tuberculosis PknB kinase domain (L33E mutant) in… · the same entry in another collection · chain C against C, TM-score 1.00
P9WJA9 · AlphaFold monomer V2.0 prediction for glycogen accumulation regulator gara (P9WJA9) · a predicted model of the same protein · chain E against A, TM-score 0.94
P9WI81 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pknb (P9WI81) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P9WI81
Every structure of UniProt P9WJA9
Elsewhere: RCSB PDB 6I2P · PDBe 6I2P · UniProt P9WI81 · UniProt P9WJA9

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