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Crystal structure of DPO4 in complex with S-mc-dadp opposite dt

Analyse Crystal structure of DPO4 in complex with S-mc-dadp opposite dt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GC7
Type: protein + DNA
Length: 739 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DNA (5'-D(*G*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3'); DNA (5'…
EC: 2.7.7.7
UniProt: Q97W02
Ligands: 0OJ, CA
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA polymerase IV (EC 2.7.7.7)	protein	341	44% helix, 23% strand	Q97W02
C, E	DNA (5'-D(GGPGPGPGPAPAPGPGPAPTPTPCPC)-3')	dna	13	—	—
D	DNA (5'- D(TPCPAPTPGPGPAPAPTPCPCPTPTPCPCPCPCPC)-3')	dna	15	—	—
F	DNA (5'- D(TPCPAPTPGPGPAPAPTPCPCPTPTPCPCPCPCPC)-3')	dna	16	—	—

Ligands and binding sites

0OJ · South-methanocarba-2'-deoxyadenosine triphosphate · ligand · 2 copies · chains A, C, D, B, E, F
CA · Calcium ion · metal · 9 copies · chains A, C, B, E

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

Pockets

7 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	1056	0.81	0.83	73	0OJ, CA
2	805	0.81	0.84	65	0OJ, CA
3	580	0.75	0.83	41	empty
4	686	0.74	0.80	43	empty
5	83	0.46	0.82	14	CA

Interfaces

10 interfaces between chains.

B–F · 976 Å² buried · 23 hydrogen bonds · protein-nucleic
A–D · 943 Å² buried · 22 hydrogen bonds · protein-nucleic
B–E · 622 Å² buried · 22 hydrogen bonds · protein-nucleic
A–C · 617 Å² buried · 19 hydrogen bonds · protein-nucleic
E–F · 566 Å² buried · 60 hydrogen bonds · nucleic-nucleic

Compared structures

4GC7 · Crystal structure of Dpo4 in complex with S-MC-dADP opposite dT · the same entry in another collection · chain F against F, TM-score 1.00
Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q97W02
Elsewhere: RCSB PDB 4GC7 · PDBe 4GC7 · UniProt Q97W02

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