Protein profile

KP13_04696

Periplasmic oligopeptide-binding protein oppA

Genome: KpKP13

Gene: AHE44045.1 oppA Structure source: AlphaFold + ColabFold UniProt A0A0H3GZH5
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Amino acids 544
Annotations 6
Features 23
PDB binders 19
Druggability 0.862

Overview

Basic information about this protein and its source genome.

Accession
KP13_04696
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE44045.1 oppA
Status
annotated
Amino acids
544
Structure source
AlphaFold + ColabFold
GO
GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. GO:1904680 Enables the transfer of a peptide from one side of a membrane to the other. GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
48.237
DEG E-value
0.0
Localization
Periplasmic
ColabFold pLDDT
94.84

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 0.862
Structure A0A0H3GZH5
Pocket Pocket 1
P2Rank 0.956
Structure A0A0H3GZH5
Pocket Pocket 1
ColabFold model
FPocket 0.883 · Pocket 1
P2Rank 0.967 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 134 / 4744 genomes with a hit
Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:1904680 Enables the transfer of a peptide from one side of a membrane to the other.
  • GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
9 20 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
187 305 FunFam G3DSA:3.40.190.10:FF:000018 Oligopeptide ABC transporter, oligopeptide-binding protein
71 195 FunFam G3DSA:3.90.76.10:FF:000001 Oligopeptide ABC transporter substrate-binding protein
35 526 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
83 464 Pfam PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle
83 464 InterPro IPR000914 Solute-binding protein family 5 domain
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
71 195 Gene3D G3DSA:3.90.76.10 -
1 26 SignalP_EUK SignalP-noTM SignalP-noTM
298 513 Gene3D G3DSA:3.10.105.10 -
88 109 ProSitePatterns PS01040 Bacterial extracellular solute-binding proteins, family 5 signature.
88 109 InterPro IPR023765 Solute-binding protein family 5, conserved site
27 544 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
39 541 CDD cd08504 PBP2_OppA
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
298 514 FunFam G3DSA:3.10.105.10:FF:000001 Oligopeptide ABC transporter, oligopeptide-binding protein
41 525 Gene3D G3DSA:3.40.190.10 -
1 543 PIRSF PIRSF002741 MppA
1 543 InterPro IPR030678 Peptide/nickel binding protein, MppA-type
1 26 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
12 542 PANTHER PTHR30290 PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER
12 542 InterPro IPR039424 Solute-binding protein family 5
21 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.

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_A0A0H3GZH5
AlphaFold — — full sequence — Viewing
ColabFold KP13_04696
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
1 0.862
30 0.608
3 0.328

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 32.64 0.944
2 4.56 0.196
3 3.98 0.158
4 1.96 0.041
5 1.81 0.034

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.

69 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
6RP
5L8D
P33590 192.2 Da LogP 0.21 TPSA 72.9 ✓ Ro5 ✓ Clean c1cnn(c1)C(C(=O)O)n2cccn2
9YH
5ON0
P33590 448.5 Da LogP 2.60 TPSA 110.5 ✓ Ro5 Alert COc1cccc(c1O)CN(CCN(Cc2ccccc2SC)CC(=O)O)CC(=O)O
9YK
5ON1
P33590 434.5 Da LogP 2.29 TPSA 121.5 ✓ Ro5 Alert CSc1ccccc1CN(CCN(Cc2cccc(c2O)O)CC(=O)O)CC(=O)O
BHN
3MVZ
P33590 388.4 Da LogP 1.57 TPSA 121.5 ✓ Ro5 Alert c1ccc(c(c1)C[N@@](CC[N@](Cc2ccccc2O)CC(=O)O)CC(…
BHR
3MW0
P33590 404.4 Da LogP 1.28 TPSA 141.8 ✓ Ro5 Alert c1ccc(c(c1)C[N@@](CC[N@](Cc2cccc(c2O)O)CC(=O)O)…
BHZ
3MVW
P33590 372.4 Da LogP 1.87 TPSA 101.3 ✓ Ro5 Alert c1ccc(cc1)C[N@@](CC[N@](Cc2ccccc2O)CC(=O)O)CC(=…
CMO
5L8D
P33590 28.0 Da LogP -0.04 TPSA 19.9 ✓ Ro5 ✓ Clean [C-]#[O+]
DTD
3MW0
P33590 152.2 Da LogP 0.10 TPSA 40.5 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](CSS1)O)O
DTT
1ZLQ
P33590 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
DTU
3MVX
P33590 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@H](CS)O)O)S
DTV
3MVX
P33590 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@@H](CS)O)O)S
EDT
1ZLQ
P33590 292.2 Da LogP -2.07 TPSA 155.7 ✓ Ro5 ✓ Clean C(CN(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O
GDS
3M8U
B8F653 612.6 Da LogP -3.88 TPSA 317.6 3 viol. ✓ Clean C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)…
HCT
3DP8
P33590 190.2 Da LogP 0.03 TPSA 111.9 ✓ Ro5 ✓ Clean C(CC(=O)O)[C@H](CC(=O)O)C(=O)O
IUM
1B40
P06202 270.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][U+4][O-]
MHI
3O9P
P77348 390.4 Da LogP -2.17 TPSA 222.1 1 viol. ✓ Clean C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=…
MLI
3M8U
B8F653 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PER
3MVZ
P33590 32.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][O-]
U1
1B05
P06202 238.0 Da LogP 0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [U]

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.