Protein profile

PA1529

NAD-dependent DNA ligase LigA

Genome: NC_002516.2

Gene: lig Structure source: ColabFold
Amino acids 794
Annotations 3
Features 59
PDB binders 7
Druggability 0.683

Overview

Basic information about this protein and its source genome.

Accession
PA1529
Gene
lig
Status
annotated
Amino acids
794
Structure source
ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
51.389
Human E-value
3.91e-11
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 0.683
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MTDTQAAAERIAQLRTELDTHNYRYYVLDEPSIPDAEYDRLFRELQALEAEYPQLLTPDSPTQRVSGTPASAFGEVRHEIPMLSLGNAFEEQDLLDFDRRVREGLADLLPGGDLLGGGAEVEYSCEPKLDGLAVSLLYERGQLVRGATRGDGSTGEDITSNVRTIRNVPLKLHGEGWPEILEVRGEVFMSKAGFEALNAKAVETGGKTFANPRNAAAGSLRQLDSKITASRPLEFCAYGFGQVSGTLPDTQVGILEAFRGWGIPISRELRLVKGAQACRDYYDDIGRRRDALAYEIDGVVFKVNRIAFQRELGFRAREPRWAIAHKFPAREELTELLGVEFQVGRTGAVTPVARLKPVQVAGVTVSNATLHNMDEVARLGLRIGDTVVIRRAGDVIPQVMQVVLERRPADAQAIEVPEHCPVCGSAVERTQLVKRSKGKESISEGAIYRCVGRLSCQAQLKQAIIHFVSRRAMDIDGLGDKIVEQLVDRGLVASPADLYTLTYEQVFELEGFAELSTNNLLTAIADSRKPSLARFIFALGIPDVGEETAKLLARSLGSLERIGKALPEVLTYLPDVGAEVAYEIHNFFADEHNRQVIAQLRDAEHGVQLQEEGEVAAEFAACASLAGFIDKLNIPFIAATGAEKLASRFGSLDGIIRADWLDLRQVERLPERAAKSLRDFFDEPANVQRALAIEAQLREFGMHWQSERKAVEGLPLAGQTWVLTGTLEAMSRDVAKDKLEGLGAKVAGSVSAKTHCVVAGPGAGSKLAKANELGVKVLDEDGLLKLFDEHGVAR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • 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.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0003911 Catalysis of the reaction: NAD+ + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + nicotinamide nucleotide + deoxyribonucleotide(n+m).

Sequence Features

Domain/signature hits from InterPro and related databases.

59 records
Show feature table
Start End DB Term Name
454 528 Gene3D G3DSA:1.10.150.20 -
702 788 Gene3D G3DSA:3.40.50.10190 BRCT domain
702 788 InterPro IPR036420 BRCT domain superfamily
16 770 PANTHER PTHR23389 CHROMOSOME TRANSMISSION FIDELITY FACTOR 18
454 529 FunFam G3DSA:1.10.150.20:FF:000007 DNA ligase
416 603 SUPERFAMILY SSF47781 RuvA domain 2-like
416 603 InterPro IPR010994 RuvA domain 2-like
329 402 Gene3D G3DSA:2.40.50.140 -
329 402 InterPro IPR012340 Nucleic acid-binding, OB-fold
419 458 Pfam PF03119 NAD-dependent DNA ligase C4 zinc finger domain
419 458 InterPro IPR004149 Zinc-finger, NAD-dependent DNA ligase C4-type
330 412 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
330 412 InterPro IPR012340 Nucleic acid-binding, OB-fold
329 402 FunFam G3DSA:2.40.50.140:FF:000012 DNA ligase
706 789 FunFam G3DSA:3.40.50.10190:FF:000069 DNA ligase
624 701 Gene3D G3DSA:1.10.150.20 -
620 792 PIRSF PIRSF001604 LigA
620 792 InterPro IPR001679 NAD-dependent DNA ligase
1 622 PIRSF PIRSF001604 LigA
1 622 InterPro IPR001679 NAD-dependent DNA ligase
128 157 ProSitePatterns PS01055 NAD-dependent DNA ligase signature 1.
128 157 InterPro IPR018239 NAD-dependent DNA ligase, active site
2 67 FunFam G3DSA:1.10.287.610:FF:000002 DNA ligase
403 453 Gene3D G3DSA:6.20.10.30 -
343 358 ProSitePatterns PS01056 NAD-dependent DNA ligase signature 2.
343 358 InterPro IPR033136 NAD-dependent DNA ligase, conserved site
714 788 SUPERFAMILY SSF52113 BRCT domain
714 788 InterPro IPR036420 BRCT domain superfamily
5 787 Hamap MF_01588 DNA ligase [ligA].
5 787 InterPro IPR001679 NAD-dependent DNA ligase
1 67 Gene3D G3DSA:1.10.287.610 Helix hairpin bin
716 786 CDD cd17748 BRCT_DNA_ligase_like
713 790 SMART SM00292 BRCT_7
713 790 InterPro IPR001357 BRCT domain
6 472 SMART SM00532 ligaN3
6 472 InterPro IPR013840 NAD-dependent DNA ligase, N-terminal
7 330 Pfam PF01653 NAD-dependent DNA ligase adenylation domain
7 330 InterPro IPR013839 NAD-dependent DNA ligase, adenylation
3 328 SUPERFAMILY SSF56091 DNA ligase/mRNA capping enzyme, catalytic domain
713 787 Pfam PF00533 BRCA1 C Terminus (BRCT) domain
713 787 InterPro IPR001357 BRCT domain
334 410 Pfam PF03120 NAD-dependent DNA ligase OB-fold domain
334 410 InterPro IPR004150 NAD-dependent DNA ligase, OB-fold
68 327 Gene3D G3DSA:3.30.470.30 DNA ligase/mRNA capping enzyme
711 794 ProSiteProfiles PS50172 BRCT domain profile.
711 794 InterPro IPR001357 BRCT domain
530 609 FunFam G3DSA:1.10.150.20:FF:000006 DNA ligase
632 687 Pfam PF12826 Helix-hairpin-helix motif
632 687 InterPro IPR041663 DisA/LigA, helix-hairpin-helix motif
534 597 Pfam PF12826 Helix-hairpin-helix motif
534 597 InterPro IPR041663 DisA/LigA, helix-hairpin-helix motif
618 704 SUPERFAMILY SSF47781 RuvA domain 2-like
618 704 InterPro IPR010994 RuvA domain 2-like
68 327 FunFam G3DSA:3.30.470.30:FF:000001 DNA ligase
14 617 NCBIfam TIGR00575 DNA ligase (NAD(+)) LigA
14 617 InterPro IPR001679 NAD-dependent DNA ligase
529 611 Gene3D G3DSA:1.10.150.20 -
9 329 CDD cd00114 LIGANc
9 329 InterPro IPR013839 NAD-dependent DNA ligase, adenylation

3D Structure

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

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
ColabFold PA1529
ColabFold full sequence Viewing
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
1 0.683

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.

58 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
0XS P15042 335.1 Da LogP 2.09 TPSA 94.9 ✓ Ro5 ✓ Clean c1c2cc(c(nc2nc(c1C(=O)N)N)C(F)(F)F)Br
0XT C1CKI0 206.2 Da LogP -0.10 TPSA 112.8 ✓ Ro5 ✓ Clean Cc1c(nc2c(n1)c(nc(n2)N)N)OC
1X7 Q837V6 272.1 Da LogP 1.74 TPSA 82.0 ✓ Ro5 ✓ Clean c1c2c(c(cnc2N)C(=O)N)sc1Br
1X8 Q837V6 236.3 Da LogP 0.08 TPSA 125.1 ✓ Ro5 ✓ Clean c1c2c(c(cnc2N)C(=O)N)sc1C(=O)N
IVH P43813 355.4 Da LogP -0.09 TPSA 139.5 ✓ Ro5 ✓ Clean CCCCSc1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H…
IWH P43813 256.3 Da LogP 1.61 TPSA 65.1 ✓ Ro5 ✓ Clean Cc1ccc(c(c1)C)CN2C=C(C=CC2=O)C(=O)N
NMN Q837V6 335.2 Da LogP -2.20 TPSA 163.4 ✓ Ro5 ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…

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.