MolNFT v1 · #122109 · protein + DNA

Crystal structure of R.PABI-nonspecific DNA complex

5IFF · Uncharacterized protein: “Crystal structure of R.PABI-nonspecific DNA complex”. X-ray diffraction, 3 pockets (best druggability 0.81). MolNFT v1 #122109 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IFF
Type: protein + DNA
Length: 448 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein; DNA (5'- D(*GP*CP*AP*CP*TP*AP*GP*TP*TP*CP*GP*AP*AP*CP*TP*AP*GP*TP…
UniProt: Q9V2B6
Pockets: 3 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein	protein	216	31% helix, 36% strand	Q9V2B6
B	Uncharacterized protein	protein	212	27% helix, 37% strand	Q9V2B6
C	DNA (5'- D(GPCPAPCPTPAPGPTPTPCPGPAPAPCPTPAPGPTPGPC)-3')	dna	20	—	—

Pockets

3 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	1173	0.81	0.82	98	empty
2	67	0.32	0.75	11	empty
3	51	0.29	0.76	16	empty

Interfaces

3 interfaces between chains.

A–B · 1773 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 252 Å² buried · 6 hydrogen bonds · protein-nucleic
B–C · 192 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

5IFF · Crystal structure of R.PabI-nonspecific DNA 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 Q9V2B6
Elsewhere: RCSB PDB 5IFF · PDBe 5IFF · UniProt Q9V2B6

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