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I-onui K227Y, D236A bound to A3G substrate (pre-cleavage complex)

Analyse I-onui K227Y, D236A bound to A3G substrate (pre-cleavage complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BDB
Type: protein + DNA
Length: 347 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal protein 3/HOMING endonuclease-like protein fusion; DNA (26-mer)
UniProt: Q4VWW5
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosomal protein 3/HOMING endonuclease-like protein fusion	protein	295	49% helix, 22% strand	Q4VWW5
B	DNA (26-mer)	dna	26	—	—
C	DNA (26-mer)	dna	26	—	—

Pockets

6 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	186	0.75	0.92	27	empty
2	170	0.57	0.82	24	empty
3	104	0.49	0.81	19	empty
4	66	0.46	0.83	19	empty
5	101	0.40	0.77	22	empty

Interfaces

3 interfaces between chains.

A–B · 1594 Å² buried · 26 hydrogen bonds · protein-nucleic
A–C · 1482 Å² buried · 29 hydrogen bonds · protein-nucleic
B–C · 1237 Å² buried · 97 hydrogen bonds · nucleic-nucleic

Compared structures

6BDB · I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex) · 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 Q4VWW5
Elsewhere: RCSB PDB 6BDB · PDBe 6BDB · UniProt Q4VWW5

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