MolNFT v1 · #21070 · protein + DNA

Replication of a cis-syn thymine dimer at atomic resolution

1RYS · 5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*A)-3': “Replication of a cis-syn thymine dimer at atomic resolution”. X-ray diffraction, 3 ligands (ATP, CA, NA), 5 pockets (best druggability 0.80). MolNFT v1 #21070 on GenesisL1: 3D…

PDB: 1RYS
Type: protein + DNA
Length: 743 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*A)-3'…
EC: 2.7.7.7
UniProt: Q97W02
Ligands: ATP, CA, NA
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E	5'-D(GPGPGPGPAPAPGPGPAPTPTPCP*A)-3'	dna	13	—	—
D	5'-D(TPCPTPTPTPGPAPAPTPCPCPTPTPCPCPCPCPC) -3'	dna	17	—	—
F	5'-D(TPCPTPTPTPGPAPAPTPCPCPTPTPCPCPCPCPC) -3'	dna	18	—	—
A, B	DNA polymerase IV (EC 2.7.7.7)	protein	341	44% helix, 25% strand	Q97W02

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, D, A, E, F, B
CA · Calcium ion · metal · 5 copies · chains C, A, B, E
NA · Sodium ion · metal · chains F, B
EDO · 1,2-ethanediol · additive · chains E, F, B

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

Pockets

5 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	1157	0.80	0.82	87	EDO, CA, ATP
2	1195	0.77	0.79	82	CA, ATP
3	588	0.75	0.82	43	empty
4	456	0.73	0.83	42	empty
5	86	0.32	0.73	17	empty

Interfaces

8 interfaces between chains.

F–B · 1025 Å² buried · 23 hydrogen bonds · protein-nucleic
D–A · 878 Å² buried · 22 hydrogen bonds · protein-nucleic
E–B · 601 Å² buried · 19 hydrogen bonds · protein-nucleic
C–D · 580 Å² buried · 47 hydrogen bonds · nucleic-nucleic
E–F · 574 Å² buried · 52 hydrogen bonds · nucleic-nucleic

Compared structures

1RYS · Replication of a cis-syn thymine dimer at atomic resolution · the same entry in another collection · chain B against B, TM-score 1.00
Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A 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 1RYS · PDBe 1RYS · UniProt Q97W02

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