English 日本語简体中文繁體中文 한국어

✖

Menu

RCSB PDB PDBe BMRB Adv. Search Search help

Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5F3C

Crystal structure of human KDM4A in complex with compound 52d

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN A 401

Chain	Residue
A	HIS188
A	GLU190
A	HIS276
A	5U8403
A	HOH504

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 402

Chain	Residue
A	CYS234
A	HIS240
A	CYS306
A	CYS308

site_id	AC3
Number of Residues	17
Details	binding site for residue 5U8 A 403

Chain	Residue
A	GLN73
A	ASN86
A	TYR132
A	ASP135
A	GLU169
A	GLY170
A	TYR177
A	SER184
A	PHE185
A	HIS188
A	GLU190
A	LYS206
A	TRP208
A	LYS241
A	HIS276
A	ZN401
A	HOH504

site_id	AC4
Number of Residues	5
Details	binding site for residue DMS A 404

Chain	Residue
A	TYR59
A	ARG98
A	PHE202
A	PHE283
A	HOH522

site_id	AC5
Number of Residues	2
Details	binding site for residue DMS A 405

Chain	Residue
A	GLN88
A	LYS90

site_id	AC6
Number of Residues	1
Details	binding site for residue DMS A 406

Chain	Residue
A	TRP332

site_id	AC7
Number of Residues	1
Details	binding site for residue DMS A 407

Chain	Residue
A	PHE324

site_id	AC8
Number of Residues	7
Details	binding site for residue GOL A 408

Chain	Residue
A	PRO49
A	PRO50
A	ALA264
A	GLY265
A	GLU266
A	HOH511
A	HOH552

site_id	AC9
Number of Residues	5
Details	binding site for residue ZN B 401

Chain	Residue
B	HIS188
B	GLU190
B	HIS276
B	5U8403
B	HOH505

site_id	AD1
Number of Residues	4
Details	binding site for residue ZN B 402

Chain	Residue
B	CYS234
B	HIS240
B	CYS306
B	CYS308

site_id	AD2
Number of Residues	15
Details	binding site for residue 5U8 B 403

Chain	Residue
B	GLN73
B	ASN86
B	TYR132
B	ASP135
B	GLY170
B	TYR177
B	SER184
B	PHE185
B	HIS188
B	GLU190
B	LYS206
B	TRP208
B	HIS276
B	ZN401
B	HOH505

site_id	AD3
Number of Residues	4
Details	binding site for residue DMS B 404

Chain	Residue
B	GLU23
B	ARG29
B	TYR33
B	PHE353

site_id	AD4
Number of Residues	4
Details	binding site for residue DMS B 405

Chain	Residue
B	TYR111
B	PHE114
B	THR261
B	HIS281

site_id	AD5
Number of Residues	2
Details	binding site for residue DMS B 406

Chain	Residue
B	ASN86
B	MET242

site_id	AD6
Number of Residues	5
Details	binding site for residue ZN C 401

Chain	Residue
C	HIS188
C	GLU190
C	HIS276
C	5U8403
C	HOH502

site_id	AD7
Number of Residues	4
Details	binding site for residue ZN C 402

Chain	Residue
C	CYS234
C	HIS240
C	CYS306
C	CYS308

site_id	AD8
Number of Residues	13
Details	binding site for residue 5U8 C 403

Chain	Residue
C	GLN73
C	TYR132
C	ASP135
C	TYR177
C	SER184
C	PHE185
C	HIS188
C	GLU190
C	LYS206
C	TRP208
C	HIS276
C	ZN401
C	HOH502

site_id	AD9
Number of Residues	2
Details	binding site for residue DMS C 404

Chain	Residue
C	ARG98
C	TYR59

site_id	AE1
Number of Residues	2
Details	binding site for residue DMS C 405

Chain	Residue
C	TRP332
C	LYS333

site_id	AE2
Number of Residues	4
Details	binding site for residue ZN D 401

Chain	Residue
D	HIS188
D	GLU190
D	HIS276
D	5U8403

site_id	AE3
Number of Residues	4
Details	binding site for residue ZN D 402

Chain	Residue
D	CYS234
D	HIS240
D	CYS306
D	CYS308

site_id	AE4
Number of Residues	12
Details	binding site for residue 5U8 D 403

Chain	Residue
D	TYR132
D	ASP135
D	TYR175
D	TYR177
D	PHE185
D	HIS188
D	GLU190
D	LYS206
D	TRP208
D	HIS276
D	ZN401
D	HOH704

site_id	AE5
Number of Residues	4
Details	binding site for residue DMS D 404

Chain	Residue
D	LYS217
D	GLN302
D	HOH502
D	HOH514

site_id	AE6
Number of Residues	2
Details	binding site for residue DMS D 405

Chain	Residue
D	ARG294
D	GLN325

site_id	AE7
Number of Residues	1
Details	binding site for residue CL D 406

Chain	Residue
D	ARG98

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:16677698

Chain	Residue	Details
A	TYR132
D	TYR132
D	ASN198
D	LYS206
A	ASN198
A	LYS206
B	TYR132
B	ASN198
B	LYS206
C	TYR132
C	ASN198
C	LYS206

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00538, ECO:0000269\|PubMed:16677698, ECO:0000305\|PubMed:26741168

Chain	Residue	Details
A	HIS188
A	HIS276
B	HIS188
B	HIS276
C	HIS188
C	HIS276
D	HIS188
D	HIS276

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:16677698, ECO:0000305\|PubMed:26741168

Chain	Residue	Details
A	GLU190
B	GLU190
C	GLU190
D	GLU190

site_id	SWS_FT_FI4
Number of Residues	16
Details	BINDING: BINDING => ECO:0007744\|PDB:5F2W, ECO:0007744\|PDB:5F32, ECO:0007744\|PDB:5F37, ECO:0007744\|PDB:5F39, ECO:0007744\|PDB:5F3E, ECO:0007744\|PDB:5F3G, ECO:0007744\|PDB:5F5I

Chain	Residue	Details
A	CYS234
C	HIS240
C	CYS306
C	CYS308
D	CYS234
D	HIS240
D	CYS306
D	CYS308
A	HIS240
A	CYS306
A	CYS308
B	CYS234
B	HIS240
B	CYS306
B	CYS308
C	CYS234

site_id	SWS_FT_FI5
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:B2RXH2

Chain	Residue	Details
A	LYS241
B	LYS241
C	LYS241
D	LYS241

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: N-acetylalanine => ECO:0007744\|PubMed:19413330

Chain	Residue	Details
A	ALA2
B	ALA2
C	ALA2
D	ALA2

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
A	GLY170	hydrogen bond acceptor, steric role
A	TYR177	hydrogen bond donor, steric role
A	HIS188	metal ligand
A	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
A	HIS276	metal ligand
A	SER288	hydrogen bond donor, steric role

site_id	MCSA2
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
B	GLY170	hydrogen bond acceptor, steric role
B	TYR177	hydrogen bond donor, steric role
B	HIS188	metal ligand
B	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
B	HIS276	metal ligand
B	SER288	hydrogen bond donor, steric role

site_id	MCSA3
Number of Residues	5
Details	M-CSA 370

Chain	Residue	Details
C	TYR177	hydrogen bond donor, steric role
C	HIS188	metal ligand
C	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
C	HIS276	metal ligand
C	SER288	hydrogen bond donor, steric role

site_id	MCSA4
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
D	GLY170	hydrogen bond acceptor, steric role
D	TYR177	hydrogen bond donor, steric role
D	HIS188	metal ligand
D	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
D	HIS276	metal ligand
D	SER288	hydrogen bond donor, steric role

237423

PDB entries from 2025-06-11

PDB statistics

PDBj update info

Contact PDBj

numon