Transcription factor

Q8NHM5 - KDM2B

Lysine-specific demethylase 2B (EC 1.14.11.27) (CXXC-type zinc finger protein 2) (F-box and leucine-rich repeat protein 10) (F-box protein FBL10) (F-box/LRR-repeat protein 10) (JmjC domain-containing histone demethylation protein 1B) (Jumonji domain-containing EMSY-interactor methyltransferase motif protein) (Protein JEMMA) (Protein-containing CXXC domain 2) ([Histone-H3]-lysine-36 demethylase 1B)

Homo sapiens (Human) · Reviewed (UniProtKB/Swiss-Prot) · 1336 aa

8 Generated PWM 5 3D models

Motif Prediction

Only entries with a generated matrix are shown here.

Known1

Motif	Prediction	Source	DNA binding	Support	Logo	Actions
M01911_2.00	Known	CisBP	TATTTACGC	Direct PWM		Open · Scan

Nearest Neighbor (>70%)0

No generated PWM in this category.

Nearest Neighbor (70% - 40%)2

Motif	Prediction	Source	DNA binding	Support	Logo	Actions
M01908_2.00	NN 70-40%	CisBP	TTTGCGG	67.4% identity		Open · Scan
M01913_2.00	NN 70-40%	CisBP	GGCAGCGGGG	58.1% identity		Open · Scan

ModCRE5

Motif	Prediction	Source	DNA binding	Support	Actions
TFS_sp_Q8NHM5_KDM2B_HUMAN:608:651_3qmb_A_1	ModCRE	Homology model	GGCCCCGCGGGG	Region 608-651 · 1 3D model	Open · Scan
TFS_sp_Q8NHM5_KDM2B_HUMAN:609:722_6asb_C_1	ModCRE	Homology model	CCCCGGGCGCGG	Region 609-722 · 1 3D model	Open · Scan
TFS_sp_Q8NHM5_KDM2B_HUMAN:613:651_3qmc_A_1	ModCRE	Homology model	GGCCCCGCGGGC	Region 613-651 · 1 3D model	Open · Scan
TFS_sp_Q8NHM5_KDM2B_HUMAN:613:651_3qmd_A_1	ModCRE	Homology model	ACCCCCGCGGGC	Region 613-651 · 1 3D model	Open · Scan
TFS_sp_Q8NHM5_KDM2B_HUMAN:66:573_7uv9_K_1	ModCRE	Homology model	TTGTGGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	Region 66-573 · 1 3D model	Open · Scan

Model-supported DNA-binding regions

Protein residue intervals where structure models support predicted PWMs. Domain annotations and modeled regions are shown together when available.

1 1336 aa

66-573

608-722

Region 66-573 1 PWM

Residues: 508 aa
Domains: PF13621 · Cupin-like domain PF17811 · Jumonji helical domain
3D models: 1 active PDB · 1 summary row
Templates: 7UV9
Sources: Predicted = Low

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Region 608-722 4 PWM

Residues: 115 aa
Domains: PF02008 · CXXC zinc finger domain PF16866 · PHD-finger
3D models: 4 active PDBs · 4 summary rows
Templates: 3QMB, 3QMC, 3QMD, 6ASB
Sources: Predicted = Low

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3D Models

Collapsible technical table. Rows are grouped by protein region and retain model, template, residue coverage, and available summary evidence.

5 active PDB models 5 summary rows

Region 66-5731 model · 1 summary row

				Actions
Predicted = Low	TFS_sp_Q8NHM5_KDM2B_HUMAN:66:573_7uv9_K_1	7uv9	66-573	View model · PDB

Model-summary evidence imported for this region.

Rank	Template	Domain	N-tails	C-tails	Chains	Identity / similarity	Coverage	Model file
1	7uv9	66:573	66	573	P:K · DNA:I,J	57.9% / 67.1%	97	View · PDB TFS_sp_Q8NHM5_KDM2B_HUMAN:66:573_7uv9_K_1

Region 608-7224 models · 4 summary rows

				Actions
Predicted = Low	TFS_sp_Q8NHM5_KDM2B_HUMAN:608:651_3qmb_A_1	3qmb	608-651	View model · PDB
Predicted = Low	TFS_sp_Q8NHM5_KDM2B_HUMAN:609:722_6asb_C_1	6asb	609-722	View model · PDB
Predicted = Low	TFS_sp_Q8NHM5_KDM2B_HUMAN:613:651_3qmc_A_1	3qmc	613-651	View model · PDB
Predicted = Low	TFS_sp_Q8NHM5_KDM2B_HUMAN:613:651_3qmd_A_1	3qmd	613-651	View model · PDB

Model-summary evidence imported for this region.

Rank	Template	Domain	N-tails	C-tails	Chains	Identity / similarity	Coverage	Model file
2	6asb	66:573	609	722	P:C · DNA:A,B	79.8% / 93.0%	97	View · PDB TFS_sp_Q8NHM5_KDM2B_HUMAN:609:722_6asb_C_1
4	3qmd	66:573	613	651	P:A · DNA:B,C	65.0% / 80.0%	73	View · PDB TFS_sp_Q8NHM5_KDM2B_HUMAN:613:651_3qmd_A_1
5	3qmc	66:573	613	651	P:A · DNA:B,C	65.0% / 80.0%	73	View · PDB TFS_sp_Q8NHM5_KDM2B_HUMAN:613:651_3qmc_A_1
3	3qmb	66:573	608	651	P:A · DNA:B,C	60.0% / 73.3%	81	View · PDB TFS_sp_Q8NHM5_KDM2B_HUMAN:608:651_3qmb_A_1

View full model evidence table for rank, chains, N/C tails, coverage, RMSD-template information, identity/similarity, and linked model files.

Domains

Annotated protein domains. Overlaps with model-supported DNA-binding regions are shown when available.

Residues	PFAM	Domain	Used by prediction region?
142-318	PF13621	Cupin-like domain	overlaps 66-573
334-373	PF17811	Jumonji helical domain	overlaps 66-573
607-651	PF02008	CXXC zinc finger domain	overlaps 608-722
656-722	PF16866	PHD-finger	overlaps 608-722
1068-1107	PF12937	F-box-like	No overlap with loaded model regions
1210-1314	PF25372	F-box/LRR-repeat protein 15, leucine rich repeat domain	No overlap with loaded model regions