MolNFT v1 · #102718 · protein + DNA

Crystal structure of DNAT84-153-DT10 ssdna complex form 1

4OU6 · Primosomal protein 1: “Crystal structure of DNAT84-153-DT10 ssdna complex form 1”. X-ray diffraction, 4 pockets (best druggability 0.73). MolNFT v1 #102718 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OU6
Type: protein + DNA
Length: 369 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Primosomal protein 1; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
UniProt: P0A8J2
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Primosomal protein 1	protein	76	47% helix, 8% strand	P0A8J2
B, D, E	Primosomal protein 1	protein	71	54% helix, 6% strand	P0A8J2
C	Primosomal protein 1	protein	70	51% helix, 6% strand	P0A8J2
L	DNA (5'-D(PTPTPTPTPTPTPTPTPTPT)-3')	dna	10	—	—

Pockets

4 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	339	0.73	0.85	41	empty
2	230	0.66	0.84	29	empty
3	327	0.65	0.80	35	empty
4	160	0.59	0.83	28	empty

Interfaces

9 interfaces between chains.

A–B · 425 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 424 Å² buried · 8 hydrogen bonds · protein-protein
C–L · 394 Å² buried · 9 hydrogen bonds · protein-nucleic
A–C · 386 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 366 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4OU6 · Crystal structure of DnaT84-153-dT10 ssDNA complex form 1 · the same entry in another collection · chain L against L, TM-score 1.00
P0A8J2 · AlphaFold monomer V2.0 prediction for primosomal protein 1 (P0A8J2) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P0A8J2
Elsewhere: RCSB PDB 4OU6 · PDBe 4OU6 · UniProt P0A8J2

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