Protein profile

PA0002

DNA polymerase III subunit beta

Genome: NC_002516.2

Gene: PA0002 dnaN Structure source: Experimental + AlphaFold UniProt Q9I7C4
Amino acids 367
Annotations 8
Features 26
PDB binders 19
Druggability 0.936

Overview

Basic information about this protein and its source genome.

Accession
PA0002
Gene
PA0002 dnaN
Status
annotated
Amino acids
367
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.936
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009360 The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
  • GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0006271 The process in which an existing DNA strand is extended by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
126 245 SUPERFAMILY SSF55979 DNA clamp
126 245 InterPro IPR046938 DNA clamp superfamily
1 123 Gene3D G3DSA:3.10.150.10 DNA Polymerase III, subunit A, domain 2
1 123 FunFam G3DSA:3.10.150.10:FF:000001 Beta sliding clamp
1 366 CDD cd00140 beta_clamp
1 366 InterPro IPR001001 DNA polymerase III, beta sliding clamp
1 367 PIRSF PIRSF000804 DNA_pol_III_b
1 367 InterPro IPR001001 DNA polymerase III, beta sliding clamp
247 366 Pfam PF02768 DNA polymerase III beta subunit, C-terminal domain
247 366 InterPro IPR022635 DNA polymerase III, beta sliding clamp, C-terminal
249 367 FunFam G3DSA:3.10.150.10:FF:000003 Beta sliding clamp
125 248 Gene3D G3DSA:3.10.150.10 DNA Polymerase III, subunit A, domain 2
1 367 NCBIfam TIGR00663 DNA polymerase III subunit beta
124 248 FunFam G3DSA:3.10.150.10:FF:000002 Beta sliding clamp
130 244 Pfam PF02767 DNA polymerase III beta subunit, central domain
130 244 InterPro IPR022637 DNA polymerase III, beta sliding clamp, central
1 367 PANTHER PTHR30478 DNA POLYMERASE III SUBUNIT BETA
17 363 SMART SM00480 pol35
17 363 InterPro IPR001001 DNA polymerase III, beta sliding clamp
1 120 SUPERFAMILY SSF55979 DNA clamp
1 120 InterPro IPR046938 DNA clamp superfamily
246 367 SUPERFAMILY SSF55979 DNA clamp
246 367 InterPro IPR046938 DNA clamp superfamily
249 367 Gene3D G3DSA:3.10.150.10 DNA Polymerase III, subunit A, domain 2
1 119 Pfam PF00712 DNA polymerase III beta subunit, N-terminal domain
1 119 InterPro IPR022634 DNA polymerase III, beta sliding clamp, N-terminal

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

4 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 4TR8
X-ray 1.80 Å A,B
100.0% 1-367
Viewing
PDB 4TSZ
X-ray 2.00 Å A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
100.0% 1-367
Loaded
PDB 6AMS
X-ray 2.39 Å A,B,C,D
100.0% 1-367
Loaded
PDB 6PTH
X-ray 3.05 Å A
100.0% 1-367
Loaded
AlphaFold PA0002
AlphaFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
7 0.936
3 0.728
8 0.505
6 0.226

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 1.69 0.029
2 1.51 0.022
3 1.33 0.015
4 0.97 0.005

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

74 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
0LA O25242 273.7 Da LogP 4.16 TPSA 53.1 ✓ Ro5 ✓ Clean C[C@@H](c1ccc2c3cc(ccc3[nH]c2c1)Cl)C(=O)O
1FL O25242 250.2 Da LogP 3.04 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(c(cc1c2ccc(cc2F)F)C(=O)O)O
27O P0A988 282.4 Da LogP 5.08 TPSA 37.3 1 viol. ✓ Clean C[C@H](c1ccc(c2c1cccc2)C3CCCCC3)C(=O)O
27R P0A988 334.2 Da LogP 2.89 TPSA 80.4 ✓ Ro5 Alert c1cc(c(c(c1)C(=O)c2ccc(cc2)Br)N)CC(=O)O
2HO P0A988 157.1 Da LogP 1.06 TPSA 43.1 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)N)F)F
2HQ P0A988 181.6 Da LogP 1.47 TPSA 46.2 ✓ Ro5 ✓ Clean c1cc2c(cc1Cl)C(=O)C(=O)N2
2HU P0A988 162.1 Da LogP 2.08 TPSA 58.9 ✓ Ro5 ✓ Clean c1cc2c(cc[nH]2)cc1[N+](=O)[O-]
2J1 P0A988 249.7 Da LogP 3.40 TPSA 53.1 ✓ Ro5 Alert c1c2c(cc(c1Cl)C(=O)O)[nH]c3c2CCCC3
2J2 P0A988 249.7 Da LogP 3.33 TPSA 53.1 ✓ Ro5 ✓ Clean c1cc2c(cc1Cl)c3c([nH]2)[C@@H](CCC3)C(=O)O
322 P0A988 499.2 Da LogP 3.17 TPSA 87.1 ✓ Ro5 Alert CCOc1cc(c(c(c1O)Br)Br)C[C@@H]2C(=O)N(C(=S)S2)CC…
323 P0A988 414.5 Da LogP 2.48 TPSA 76.6 ✓ Ro5 ✓ Clean CN(C)c1ccc2c(c1)OC3=CC(=[N+](C)C)C=CC3=C2c4ccc(…
4FC P0A988 216.2 Da LogP 3.19 TPSA 37.3 ✓ Ro5 ✓ Clean c1cc(ccc1c2ccc(cc2)F)C(=O)O
5CY P0A988 471.7 Da LogP 5.62 TPSA 46.7 1 viol. ✓ Clean CC1(c2ccccc2[N+](=C1/C=C/C=C/C=C/3\C(c4ccccc4N3…
6NI P0A988 163.1 Da LogP 1.47 TPSA 71.8 ✓ Ro5 ✓ Clean c1cc2cn[nH]c2cc1[N+](=O)[O-]
743 P0A988 434.5 Da LogP 5.49 TPSA 79.5 1 viol. ✓ Clean CCCC(=NOCc1ccc(cc1)c2ccc(cc2)F)C3C(=O)CC(C(C3=O…
BU3 P9WNU1 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
MLU P9WNU1 145.2 Da LogP 0.71 TPSA 49.3 ✓ Ro5 ✓ Clean CC(C)C[C@H](C(=O)O)NC
P4C P0A988 324.4 Da LogP -0.72 TPSA 92.7 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCC=O)O
SFK P0A988 263.3 Da LogP 2.23 TPSA 66.4 ✓ Ro5 ✓ Clean CC(C)CCC(=O)N[C@@H](Cc1ccccc1)C(=O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.