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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5F32

Crystal structure of human KDM4A in complex with compound 40

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	5V7403
A	HOH520

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	12
Details	binding site for residue 5V7 A 403

Chain	Residue
A	TYR132
A	TYR177
A	PHE185
A	HIS188
A	GLU190
A	LYS206
A	TRP208
A	HIS276
A	ZN401
A	DMS404
A	HOH520
A	HOH566

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

Chain	Residue
A	GLY170
A	GLU190
A	SER288
A	ASN290
A	5V7403

site_id	AC5
Number of Residues	6
Details	binding site for residue EDO A 405

Chain	Residue
A	PHE27
A	ASP146
A	TRP148
A	ASN149
A	ARG152
A	LEU153

site_id	AC6
Number of Residues	11
Details	binding site for residue GOL A 406

Chain	Residue
A	VAL75
A	THR76
A	GLY77
A	THR126
A	PHE127
A	HOH526
C	VAL75
C	THR76
C	GLY77
C	THR126
C	PHE127

site_id	AC7
Number of Residues	5
Details	binding site for residue ZN B 401

Chain	Residue
B	HIS188
B	GLU190
B	HIS276
B	5V7403
B	HOH502

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN B 402

Chain	Residue
B	CYS234
B	HIS240
B	CYS306
B	CYS308

site_id	AC9
Number of Residues	13
Details	binding site for residue 5V7 B 403

Chain	Residue
B	TYR132
B	TYR177
B	PHE185
B	HIS188
B	GLU190
B	LYS206
B	TRP208
B	HIS276
B	ZN401
B	DMS404
B	HOH502
B	HOH509
B	HOH580

site_id	AD1
Number of Residues	6
Details	binding site for residue DMS B 404

Chain	Residue
B	GLY170
B	TYR175
B	TYR177
B	GLU190
B	SER288
B	5V7403

site_id	AD2
Number of Residues	6
Details	binding site for residue EDO B 405

Chain	Residue
B	ASN102
B	CYS107
B	THR108
B	GLY282
B	PHE283
B	HOH579

site_id	AD3
Number of Residues	11
Details	binding site for residue GOL B 406

Chain	Residue
B	VAL75
B	THR76
B	GLY77
B	THR126
B	PHE127
D	VAL75
D	THR76
D	GLY77
D	THR126
D	PHE127
D	HOH642

site_id	AD4
Number of Residues	5
Details	binding site for residue ZN C 401

Chain	Residue
C	HIS188
C	GLU190
C	HIS276
C	5V7403
C	HOH506

site_id	AD5
Number of Residues	4
Details	binding site for residue ZN C 402

Chain	Residue
C	CYS234
C	HIS240
C	CYS306
C	CYS308

site_id	AD6
Number of Residues	13
Details	binding site for residue 5V7 C 403

Chain	Residue
C	PHE185
C	HIS188
C	GLU190
C	LYS206
C	TRP208
C	LYS241
C	HIS276
C	ZN401
C	DMS404
C	HOH506
C	HOH575
C	TYR132
C	TYR177

site_id	AD7
Number of Residues	6
Details	binding site for residue DMS C 404

Chain	Residue
C	GLY170
C	TYR177
C	GLU190
C	SER288
C	ASN290
C	5V7403

site_id	AD8
Number of Residues	1
Details	binding site for residue DMS C 405

Chain	Residue
C	THR16

site_id	AD9
Number of Residues	4
Details	binding site for residue ZN D 401

Chain	Residue
D	HIS188
D	GLU190
D	HIS276
D	5V7403

site_id	AE1
Number of Residues	4
Details	binding site for residue ZN D 402

Chain	Residue
D	CYS234
D	HIS240
D	CYS306
D	CYS308

site_id	AE2
Number of Residues	12
Details	binding site for residue 5V7 D 403

Chain	Residue
D	TYR132
D	TYR177
D	PHE185
D	HIS188
D	GLU190
D	LYS206
D	TRP208
D	LYS241
D	HIS276
D	ZN401
D	DMS404
D	HOH595

site_id	AE3
Number of Residues	7
Details	binding site for residue DMS D 404

Chain	Residue
D	GLY170
D	TYR175
D	TYR177
D	GLU190
D	SER288
D	ASN290
D	5V7403

site_id	AE4
Number of Residues	1
Details	binding site for residue DMS D 405

Chain	Residue
D	TRP332

site_id	AE5
Number of Residues	3
Details	binding site for residue EDO D 406

Chain	Residue
D	HIS201
D	PHE202
D	HOH520

site_id	AE6
Number of Residues	2
Details	binding site for residue EDO D 407

Chain	Residue
D	PHE114
D	GLU263

site_id	AE7
Number of Residues	4
Details	binding site for residue GOL D 408

Chain	Residue
D	GLU214
D	HIS215
D	ARG218
D	HOH619

site_id	AE8
Number of Residues	3
Details	binding site for residue GOL D 409

Chain	Residue
D	LEU248
D	LYS251
D	LYS252

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	6
Details	M-CSA 370

Chain	Residue	Details
C	GLY170	hydrogen bond acceptor, steric role
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

222926

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