MolNFT v1 · #19695 · protein + DNA

Crystal structure of the complex of hmg-D and DNA

1QRV · DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'): “Crystal structure of the complex of hmg-D and DNA”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.57). MolNFT v1 #19695 on GenesisL1: 3D structure, binding sites and…

PDB: 1QRV
Type: protein + DNA
Length: 164 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'); High mobility group protein D
UniProt: Q05783
Ligands: NA
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'-D(GPCPGPAPTPAPTPCPGPC)-3')	dna	10	—	—
A	High mobility group protein D	protein	73	68% helix, 0% strand	Q05783
B	High mobility group protein D	protein	71	73% helix, 0% strand	Q05783

Ligands and binding sites

NA · Sodium ion · metal · chains C, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	187	0.57	0.81	24	empty
2	101	0.51	0.82	18	empty
3	304	0.50	0.73	28	empty

Interfaces

6 interfaces between chains.

C–A · 663 Å² buried · 13 hydrogen bonds · protein-nucleic
C–D · 445 Å² buried · 37 hydrogen bonds · nucleic-nucleic
D–A · 412 Å² buried · 4 hydrogen bonds · protein-nucleic
C–B · 193 Å² buried · 2 hydrogen bonds · protein-nucleic
D–B · 146 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

1QRV · Crystal structure of the complex of hmg-D and DNA · the same entry in another collection · chain C against C, TM-score 1.00
Q05783 · AlphaFold monomer V2.0 prediction for high mobility group protein D (Q05783) · a predicted model of the same protein · chain B against A, TM-score 0.92

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 Q05783
Elsewhere: RCSB PDB 1QRV · PDBe 1QRV · UniProt Q05783

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