Protein profile

VK055_3336

ATP synthase F1, beta subunit

Genome: KpATCC43816

Gene: atpD AIK81893.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVB4
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Amino acids 460
Annotations 10
Features 30
PDB binders 12
Druggability 0.523

Overview

Basic information about this protein and its source genome.

Accession
VK055_3336
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
atpD AIK81893.1
Status
annotated
Amino acids
460
Structure source
AlphaFold + ColabFold
EC
7.1.2.2
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0015986 The chemical reactions and pathways resulting in the formation of ATP driven by transport of protons across a membrane to generate an electrochemical gradient (proton-motive force). GO:0045261 OBSOLETE. The sector of a hydrogen-transporting ATP synthase complex in which the catalytic activity resides; it comprises the catalytic core and central stalk, and is peripherally associated with a membrane, such as the plasma membrane or the mitochondrial inner membrane, when the entire ATP synthase is assembled. GO:0046034 The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator. GO:0046933 Enables the synthesis of ATP from ADP and phosphate by the transfer of protons from one side of a membrane to the other by a rotational mechanism driven by a gradient according to the reaction: ADP + phosphate + 5 H+(out) => ATP + H2O + 4 H+(in). GO:1902600 The directed movement of a proton across a membrane.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
71.03
Human E-value
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
98.478
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
93.31

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 0.523
Structure A0A0H3GVB4
Pocket Pocket 25
P2Rank 0.615
Structure A0A0H3GVB4
Pocket Pocket 1
ColabFold model
FPocket 0.535 · Pocket 8
P2Rank 0.574 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3304 / 4744 genomes with a hit
Normalized 0.696

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0015986 The chemical reactions and pathways resulting in the formation of ATP driven by transport of protons across a membrane to generate an electrochemical gradient (proton-motive force).
  • GO:0045261 OBSOLETE. The sector of a hydrogen-transporting ATP synthase complex in which the catalytic activity resides; it comprises the catalytic core and central stalk, and is peripherally associated with a membrane, such as the plasma membrane or the mitochondrial inner membrane, when the entire ATP synthase is assembled.
  • GO:0046034 The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0046933 Enables the synthesis of ATP from ADP and phosphate by the transfer of protons from one side of a membrane to the other by a rotational mechanism driven by a gradient according to the reaction: ADP + phosphate + 5 H+(out) => ATP + H2O + 4 H+(in).
  • GO:1902600 The directed movement of a proton across a membrane.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0045259 A proton-transporting two-sector ATPase complex that catalyzes the phosphorylation of ADP to ATP during oxidative phosphorylation. The complex comprises a membrane sector (F0) that carries out proton transport and a cytoplasmic compartment sector (F1) that catalyzes ATP synthesis by a rotational mechanism; the extramembrane sector (containing 3 a and 3 b subunits) is connected via the d-subunit to the membrane sector by several smaller subunits. Within this complex, the g and e subunits and the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis. This movement is driven by the hydrogen ion electrochemical potential gradient.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
76 344 Gene3D G3DSA:3.40.50.300 -
76 344 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 460 Hamap MF_01347 ATP synthase subunit beta [atpB].
1 460 InterPro IPR005722 ATP synthase, F1 complex, beta subunit
3 460 NCBIfam TIGR01039 F0F1 ATP synthase subunit beta
3 460 InterPro IPR005722 ATP synthase, F1 complex, beta subunit
77 347 CDD cd01133 F1-ATPase_beta_CD
1 75 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase
1 75 InterPro IPR036121 ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily
349 456 CDD cd18110 ATP-synt_F1_beta_C
77 348 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
77 348 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
76 344 FunFam G3DSA:3.40.50.300:FF:000004 ATP synthase subunit beta
2 75 Gene3D G3DSA:2.40.10.170 -
2 460 PANTHER PTHR15184 ATP SYNTHASE
345 460 FunFam G3DSA:1.10.1140.10:FF:000001 ATP synthase subunit beta
450 460 Coils Coil Coil
345 460 Gene3D G3DSA:1.10.1140.10 -
345 460 InterPro IPR024034 ATPase, F1/V1 complex, beta/alpha subunit, C-terminal
2 76 CDD cd18115 ATP-synt_F1_beta_N
345 459 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase
6 72 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain
6 72 InterPro IPR004100 ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain
333 342 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature.
333 342 InterPro IPR020003 ATPase, alpha/beta subunit, nucleotide-binding domain, active site
1 75 FunFam G3DSA:2.40.10.170:FF:000003 ATP synthase subunit beta
142 327 SMART SM00382 AAA_5
142 327 InterPro IPR003593 AAA+ ATPase domain
130 342 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain
130 342 InterPro IPR000194 ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain

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_A0A0H3GVB4
AlphaFold — — full sequence — Viewing
ColabFold VK055_3336
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
25 0.523
4 0.225

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 7.9 0.419
2 4.49 0.191
3 3.63 0.136
4 2.95 0.095
5 1.82 0.035

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.

63 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
AF3
1E1R
P00829 84.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al](F)F
ALF
1H8E
P00829 103.0 Da LogP 1.30 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al-](F)(F)F
ANP
3OAA
P0ABB4 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AUR
1COW
P00829 460.5 Da LogP 3.10 TPSA 104.4 ✓ Ro5 ✓ Clean CC[C@@H]1[C@]2([C@H]([C@@](O1)([C@H]([C@@H](O2)…
AZI
2CK3
P00829 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
BEF
1W0J
P00829 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
DCW
1E79
P00829 224.3 Da LogP 2.95 TPSA 41.1 ✓ Ro5 ✓ Clean C1CCC(CC1)NC(=O)NC2CCCCC2
QUE
2JJ2
P00829 302.2 Da LogP 1.99 TPSA 131.4 ✓ Ro5 Alert c1cc(c(cc1C2=C(C(=O)c3c(cc(cc3O2)O)O)O)O)O
STL
2JIZ
P00829 228.2 Da LogP 2.97 TPSA 60.7 ✓ Ro5 ✓ Clean c1cc(ccc1\C=C\c2cc(cc(c2)O)O)O
TS6
4YXW
P00829 114.1 Da LogP 0.01 TPSA 57.5 ✓ Ro5 ✓ Clean OP(=O)(O)S
TTX
1KMH
P00825 414.5 Da LogP 0.99 TPSA 98.8 ✓ Ro5 ✓ Clean C[C@H]1C(=O)N[C@H](C(=O)N(/C(=C\c2ccccc2)/C(=O)…
VO4
2F43
P10719 114.9 Da LogP -3.69 TPSA 86.2 ✓ Ro5 ✓ Clean [O-][V](=O)([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.