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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5LY2

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3 (13-mer)

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue NI A 501

Chain	Residue
A	HIS188
A	GLU190
A	HIS276
A	OGA503
A	HOH663

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 502

Chain	Residue
A	CYS234
A	HIS240
A	CYS306
A	CYS308

site_id	AC3
Number of Residues	13
Details	binding site for residue OGA A 503

Chain	Residue
A	TYR132
A	PHE185
A	HIS188
A	GLU190
A	SER196
A	ASN198
A	LYS206
A	HIS276
A	SER288
A	NI501
A	HOH663
E	M3L6
E	HOH102

site_id	AC4
Number of Residues	2
Details	binding site for residue GOL A 504

Chain	Residue
A	ASP311
E	TYR3

site_id	AC5
Number of Residues	2
Details	binding site for residue GOL A 505

Chain	Residue
A	TYR59
A	ASP60

site_id	AC6
Number of Residues	2
Details	binding site for residue CL B 401

Chain	Residue
A	GLY229
B	LYS105

site_id	AC7
Number of Residues	5
Details	binding site for residue NI B 402

Chain	Residue
B	HIS188
B	GLU190
B	HIS276
B	OGA405
B	HOH545

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN B 403

Chain	Residue
B	CYS234
B	HIS240
B	CYS306
B	CYS308

site_id	AC9
Number of Residues	2
Details	binding site for residue CL B 404

Chain	Residue
B	GLY229
B	SER230

site_id	AD1
Number of Residues	11
Details	binding site for residue OGA B 405

Chain	Residue
B	TYR132
B	PHE185
B	HIS188
B	GLU190
B	SER196
B	ASN198
B	LYS206
B	HIS276
B	NI402
B	HOH545
F	M3L6

site_id	AD2
Number of Residues	2
Details	binding site for residue GOL B 406

Chain	Residue
B	GLY138
B	THR139

site_id	AD3
Number of Residues	8
Details	binding site for residue GOL B 407

Chain	Residue
B	ASP191
B	ARG239
B	HIS240
B	CYS306
B	VAL313
B	HOH527
F	ASN4
F	TRP9

site_id	AD4
Number of Residues	4
Details	binding site for residue GOL B 408

Chain	Residue
B	TYR85
B	ASN86
B	MET242
F	TRP9

site_id	AD5
Number of Residues	5
Details	binding site for residue NI C 501

Chain	Residue
C	HIS188
C	GLU190
C	HIS276
C	OGA504
C	HOH641

site_id	AD6
Number of Residues	4
Details	binding site for residue ZN C 502

Chain	Residue
C	CYS234
C	HIS240
C	CYS306
C	CYS308

site_id	AD7
Number of Residues	2
Details	binding site for residue CL C 503

Chain	Residue
C	TYR59
C	ARG98

site_id	AD8
Number of Residues	13
Details	binding site for residue OGA C 504

Chain	Residue
C	TYR132
C	PHE185
C	HIS188
C	GLU190
C	SER196
C	ASN198
C	LYS206
C	TRP208
C	HIS276
C	SER288
C	NI501
C	HOH641
G	HOH101

site_id	AD9
Number of Residues	2
Details	binding site for residue CL D 401

Chain	Residue
C	PHE227
D	LYS105

site_id	AE1
Number of Residues	5
Details	binding site for residue NI D 402

Chain	Residue
D	HIS188
D	GLU190
D	HIS276
D	OGA405
D	HOH528

site_id	AE2
Number of Residues	4
Details	binding site for residue ZN D 403

Chain	Residue
D	CYS234
D	HIS240
D	CYS306
D	CYS308

site_id	AE3
Number of Residues	3
Details	binding site for residue CL D 404

Chain	Residue
D	PHE227
D	GLY229
D	SER230

site_id	AE4
Number of Residues	11
Details	binding site for residue OGA D 405

Chain	Residue
D	TYR132
D	PHE185
D	HIS188
D	GLU190
D	SER196
D	ASN198
D	LYS206
D	SER288
D	NI402
D	HOH528
D	HOH561

site_id	AE5
Number of Residues	14
Details	binding site for Ligand residues M3L E 6 through SER E 7 bound to THR E 5

Chain	Residue
A	ASP135
A	GLY170
A	TYR177
A	GLU190
A	LYS241
A	SER288
A	THR289
A	ASN290
A	OGA503
E	THR5
E	GLY8
E	HOH101
E	HOH102
E	HOH103

site_id	AE6
Number of Residues	16
Details	binding site for Ligand residues M3L F 6 through SER F 7 bound to THR F 5

Chain	Residue
B	ASN86
B	ALA134
B	ASP135
B	GLY170
B	TYR177
B	GLU190
B	LYS241
B	SER288
B	THR289
B	ASN290
B	OGA405
B	HOH545
F	THR5
F	GLY8
F	HOH101
F	HOH102

site_id	AE7
Number of Residues	8
Details	binding site for Ligand residues M3L G 6 through SER G 7 bound to THR G 5

Chain	Residue
C	ASP135
C	TYR177
C	LYS241
C	SER288
C	ASN290
G	THR5
G	GLY8
G	HOH101

site_id	AE8
Number of Residues	11
Details	binding site for Ligand residues M3L H 6 through SER H 7 bound to THR H 5

Chain	Residue
D	ASP135
D	GLY170
D	TYR175
D	TYR177
D	GLU190
D	LYS241
D	SER288
D	ASN290
H	THR5
H	GLY8
H	HOH101

site_id	AE9
Number of Residues	5
Details	binding site for Di-peptide 48V E 0 and THR E 13

Chain	Residue
B	GLN88
E	DTY1
E	TYR12
F	TYR3
F	ARG10

site_id	AF1
Number of Residues	9
Details	binding site for Di-peptide 48V E 0 and DTY E 1

Chain	Residue
B	GLN88
B	LYS89
B	LYS90
B	HOH504
E	VAL2
E	TRP11
E	TYR12
E	THR13
F	TYR3

site_id	AF2
Number of Residues	10
Details	binding site for Di-peptide DTY E 1 and VAL E 2

Chain	Residue
A	ARG309
B	GLN88
B	LYS89
B	LYS90
B	HOH504
E	48V0
E	TYR3
E	ARG10
E	TRP11
E	TYR12

site_id	AF3
Number of Residues	8
Details	binding site for Di-peptide 48V G 0 and DTY G 1

Chain	Residue
D	GLN88
D	LYS90
D	HOH527
G	VAL2
G	TRP11
G	TYR12
G	THR13
H	TYR3

site_id	AF4
Number of Residues	5
Details	binding site for Di-peptide 48V G 0 and THR G 13

Chain	Residue
D	GLN88
G	DTY1
G	TYR12
H	TYR3
H	ARG10

site_id	AF5
Number of Residues	8
Details	binding site for Di-peptide DTY G 1 and VAL G 2

Chain	Residue
C	ARG309
D	LYS90
D	HOH527
G	48V0
G	TYR3
G	ARG10
G	TRP11
G	TYR12

Functional Information from SwissProt/UniProt

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

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

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
C	HIS188
C	HIS276
D	HIS188
D	HIS276
A	HIS188
A	HIS276
B	HIS188
B	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
B	CYS234
B	HIS240
B	CYS306
B	CYS308
C	CYS234
C	HIS240
C	CYS306
C	CYS308
D	CYS234
D	HIS240
D	CYS306
D	CYS308
A	CYS234
A	HIS240
A	CYS306
A	CYS308

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	HIS276	metal ligand
B	SER288	hydrogen bond donor, steric role
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

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

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PDB entries from 2024-05-15

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