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Crystal structure of the R.PABI(Y68F-K154A)-DSDNA(NONSPECIFIC) complex

Analyse Crystal structure of the R.PABI(Y68F-K154A)-DSDNA(NONSPECIFIC) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M3L
Type: protein + DNA
Length: 390 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RE_R_PAB1 domain-containing protein; DNA (5'- D(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP…
UniProt: G8ZFZ3
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RE_R_PAB1 domain-containing protein	protein	213	29% helix, 37% strand	G8ZFZ3
B	RE_R_PAB1 domain-containing protein	protein	165	35% helix, 32% strand	G8ZFZ3
C	DNA (5'- D(CPGPCPAPTPCPGPAPTPTPCPAPGPAPAPTPCPGPAPTPGPCP* G)-3')	dna	12	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	927	0.75	0.78	96	empty

Interfaces

3 interfaces between chains.

A–B · 1683 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 193 Å² buried · 2 hydrogen bonds · protein-nucleic
B–C · 76 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

6M3L · Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt G8ZFZ3
Elsewhere: RCSB PDB 6M3L · PDBe 6M3L · UniProt G8ZFZ3

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