Protein profile

KP13_03557

DNA ligase

Genome: KpKP13

Gene: ligA AHE43363.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVW8
Amino acids 671
Annotations 7
Features 62
PDB binders 9
Druggability 0.815

Overview

Basic information about this protein and its source genome.

Accession
KP13_03557
Gene
ligA AHE43363.1
Status
annotated
Amino acids
671
Structure source
AlphaFold + ColabFold
EC
GO
GO:0003911 Catalysis of the reaction: NAD+ + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + nicotinamide nucleotide + deoxyribonucleotide(n+m). 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
42.254
Human E-value
4.52e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
92.239
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
88.98

Selected Druggability evidence

AlphaFold / UniProt model

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 0.815
Structure A0A0H3GVW8
Pocket Pocket 26
P2Rank 0.874
Structure A0A0H3GVW8
Pocket Pocket 1
ColabFold model
FPocket 0.439 · Pocket 10
P2Rank 0.931 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 233 / 4744 genomes with a hit
Normalized 0.049

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0003911 Catalysis of the reaction: NAD+ + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + nicotinamide nucleotide + deoxyribonucleotide(n+m).
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

62 records
Show feature table
Start End DB Term Name
115 144 ProSitePatterns PS01055 NAD-dependent DNA ligase signature 1.
115 144 InterPro IPR018239 NAD-dependent DNA ligase, active site
317 390 FunFam G3DSA:2.40.50.140:FF:000012 DNA ligase
1 64 Gene3D G3DSA:1.10.287.610 Helix hairpin bin
480 499 SMART SM00278 HhH1_4
480 499 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
512 531 SMART SM00278 HhH1_4
512 531 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
446 465 SMART SM00278 HhH1_4
446 465 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
544 563 SMART SM00278 HhH1_4
544 563 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
407 434 Pfam PF03119 NAD-dependent DNA ligase C4 zinc finger domain
407 434 InterPro IPR004149 Zinc-finger, NAD-dependent DNA ligase C4-type
1 64 FunFam G3DSA:1.10.287.610:FF:000002 DNA ligase
596 668 Pfam PF00533 BRCA1 C Terminus (BRCT) domain
596 668 InterPro IPR001357 BRCT domain
446 502 Pfam PF14520 Helix-hairpin-helix domain
322 398 Pfam PF03120 NAD-dependent DNA ligase OB-fold domain
322 398 InterPro IPR004150 NAD-dependent DNA ligase, OB-fold
1 671 PIRSF PIRSF001604 LigA
1 671 InterPro IPR001679 NAD-dependent DNA ligase
2 669 Hamap MF_01588 DNA ligase [ligA].
2 669 InterPro IPR001679 NAD-dependent DNA ligase
598 668 CDD cd17748 BRCT_DNA_ligase_like
17 652 PANTHER PTHR23389 CHROMOSOME TRANSMISSION FIDELITY FACTOR 18
588 670 Gene3D G3DSA:3.40.50.10190 BRCT domain
588 670 InterPro IPR036420 BRCT domain superfamily
391 429 Gene3D G3DSA:6.20.10.30 -
403 583 SUPERFAMILY SSF47781 RuvA domain 2-like
403 583 InterPro IPR010994 RuvA domain 2-like
596 669 SUPERFAMILY SSF52113 BRCT domain
596 669 InterPro IPR036420 BRCT domain superfamily
331 346 ProSitePatterns PS01056 NAD-dependent DNA ligase signature 2.
331 346 InterPro IPR033136 NAD-dependent DNA ligase, conserved site
318 399 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
318 399 InterPro IPR012340 Nucleic acid-binding, OB-fold
430 505 Gene3D G3DSA:1.10.150.20 -
506 584 Gene3D G3DSA:1.10.150.20 -
593 671 ProSiteProfiles PS50172 BRCT domain profile.
593 671 InterPro IPR001357 BRCT domain
595 670 SMART SM00292 BRCT_7
595 670 InterPro IPR001357 BRCT domain
3 448 SMART SM00532 ligaN3
3 448 InterPro IPR013840 NAD-dependent DNA ligase, N-terminal
391 429 FunFam G3DSA:6.20.10.30:FF:000001 DNA ligase
4 318 Pfam PF01653 NAD-dependent DNA ligase adenylation domain
4 318 InterPro IPR013839 NAD-dependent DNA ligase, adenylation
317 390 Gene3D G3DSA:2.40.50.140 -
317 390 InterPro IPR012340 Nucleic acid-binding, OB-fold
2 316 SUPERFAMILY SSF56091 DNA ligase/mRNA capping enzyme, catalytic domain
588 670 FunFam G3DSA:3.40.50.10190:FF:000004 DNA ligase
430 504 FunFam G3DSA:1.10.150.20:FF:000007 DNA ligase
65 315 Gene3D G3DSA:3.30.470.30 DNA ligase/mRNA capping enzyme
510 573 Pfam PF12826 Helix-hairpin-helix motif
510 573 InterPro IPR041663 DisA/LigA, helix-hairpin-helix motif
505 583 FunFam G3DSA:1.10.150.20:FF:000006 DNA ligase
11 665 NCBIfam TIGR00575 DNA ligase (NAD(+)) LigA
11 665 InterPro IPR001679 NAD-dependent DNA ligase
65 315 FunFam G3DSA:3.30.470.30:FF:000001 DNA ligase
6 317 CDD cd00114 LIGANc
6 317 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.

3D visualization script Full viewer

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GVW8
AlphaFold full sequence Viewing
ColabFold KP13_03557
ColabFold 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
26 0.815

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 19.49 0.84
2 6.89 0.354
3 2.08 0.047
4 1.4 0.017
5 1.22 0.011

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.

60 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
DKR P9WNV1 214.3 Da LogP 2.25 TPSA 44.9 ✓ Ro5 ✓ Clean Cc1ccc(cc1)CNC(=O)c2ccc[nH]2
EWO P9WNV1 217.2 Da LogP 1.78 TPSA 40.7 ✓ Ro5 ✓ Clean c1cc(ccc1[C@@H]2c3c([nH]cn3)CCN2)F
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 P9WNV1 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.