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S-sad structure of dinb-DNA complex

Analyse S-sad structure of dinb-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R8U
Type: protein + DNA
Length: 746 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DNA
EC: 2.7.7.7
UniProt: Q47155
Ligands: 1FZ, MG
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 44% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	340	44% helix, 23% strand	Q47155
B	DNA polymerase IV (EC 2.7.7.7)	protein	338	44% helix, 23% strand	Q47155
V, C	DNA	dna	17	—	—
W	DNA	dna	18	—	—
D	DNA	dna	16	—	—

Ligands and binding sites

1FZ · 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine · ligand · 2 copies · chains A, V, W, B, C, D
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1105	0.79	0.81	80	1FZ, MG
2	900	0.78	0.81	62	MG, 1FZ
3	627	0.73	0.81	47	empty
4	626	0.71	0.79	46	empty
5	190	0.45	0.74	29	empty

Interfaces

7 interfaces between chains.

A–V · 899 Å² buried · 22 hydrogen bonds · protein-nucleic
B–C · 889 Å² buried · 18 hydrogen bonds · protein-nucleic
V–W · 702 Å² buried · 62 hydrogen bonds · nucleic-nucleic
C–D · 648 Å² buried · 63 hydrogen bonds · nucleic-nucleic
A–W · 572 Å² buried · 16 hydrogen bonds · protein-nucleic

Compared structures

4R8U · S-SAD structure of DINB-DNA Complex · the same entry in another collection · chain D against D, TM-score 1.00
Q47155 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q47155) · a predicted model of the same protein · 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 Q47155
Elsewhere: RCSB PDB 4R8U · PDBe 4R8U · UniProt Q47155

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