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Crystal structure of dnde from escherichia COLI B7A involved in DNA phosphorothioation modification

Analyse Crystal structure of dnde from escherichia COLI B7A involved in DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LRV
Type: protein
Length: 1,675 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA sulfur modification protein dnde
UniProt: B3HI59
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 12 distinct chains · 62% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	DNA sulfur modification protein dnde	protein	107	58% helix, 6% strand	B3HI59
B, J	DNA sulfur modification protein dnde	protein	106	62% helix, 6% strand	B3HI59
C	DNA sulfur modification protein dnde	protein	105	62% helix, 4% strand	B3HI59
E	DNA sulfur modification protein dnde	protein	102	65% helix, 5% strand	B3HI59
F	DNA sulfur modification protein dnde	protein	104	63% helix, 5% strand	B3HI59
G, H, O	DNA sulfur modification protein dnde	protein	106	62% helix, 4% strand	B3HI59
I	DNA sulfur modification protein dnde	protein	102	64% helix, 4% strand	B3HI59
K	DNA sulfur modification protein dnde	protein	104	63% helix, 5% strand	B3HI59
L	DNA sulfur modification protein dnde	protein	100	64% helix, 4% strand	B3HI59
M	DNA sulfur modification protein dnde	protein	106	60% helix, 5% strand	B3HI59
N	DNA sulfur modification protein dnde	protein	104	63% helix, 5% strand	B3HI59
P	DNA sulfur modification protein dnde	protein	104	62% helix, 6% strand	B3HI59

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1078	0.86	0.87	109	empty
2	919	0.85	0.86	84	empty
3	705	0.80	0.84	90	empty
4	405	0.72	0.83	63	empty
5	190	0.68	0.86	35	empty

Interfaces

40 interfaces between chains.

A–M · 720 Å² buried · 12 hydrogen bonds · protein-protein
B–K · 705 Å² buried · 9 hydrogen bonds · protein-protein
N–O · 677 Å² buried · 13 hydrogen bonds · protein-protein
F–P · 660 Å² buried · 10 hydrogen bonds · protein-protein
I–J · 641 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 modified (engineered).

Compared structures

4LRV · Crystal structure of DndE from Escherichia coli B7A involved in DNA phosphorothioation… · 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 B3HI59
Elsewhere: RCSB PDB 4LRV · PDBe 4LRV · UniProt B3HI59

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