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Structure of a putative chaperone protein dnaj from klebsiella pneumoniae subsp. pneumoniae mgh 78578

Analyse Structure of a putative chaperone protein dnaj from klebsiella pneumoniae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3I38
Type: protein
Length: 1,204 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative chaperone dnaj
UniProt: A6TH30
Pockets: 12 · best druggability 0.67

Structure

x-ray diffraction · 8 distinct chains · 19% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G	Putative chaperone dnaj	protein	103	18% helix, 33% strand	A6TH30
B	Putative chaperone dnaj	protein	101	19% helix, 34% strand	A6TH30
C, E, L	Putative chaperone dnaj	protein	98	19% helix, 34% strand	A6TH30
F	Putative chaperone dnaj	protein	100	23% helix, 32% strand	A6TH30
H	Putative chaperone dnaj	protein	99	19% helix, 33% strand	A6TH30
I	Putative chaperone dnaj	protein	96	20% helix, 34% strand	A6TH30
J	Putative chaperone dnaj	protein	101	19% helix, 32% strand	A6TH30
K	Putative chaperone dnaj	protein	104	18% helix, 31% strand	A6TH30

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	593	0.67	0.77	78	empty
2	198	0.46	0.74	33	empty
3	180	0.44	0.74	33	empty
4	66	0.35	0.77	16	empty
5	106	0.34	0.73	22	empty

Interfaces

17 interfaces between chains.

C–D · 2119 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 2107 Å² buried · 12 hydrogen bonds · protein-protein
K–L · 2103 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 2066 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 2066 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

3I38 · Structure of a putative chaperone protein dnaj from klebsiella pneumoniae subsp.… · 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 A6TH30
Elsewhere: RCSB PDB 3I38 · PDBe 3I38 · UniProt A6TH30

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