4D6S

crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound 5,6-Dimethylbenzimidazole

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1338

Chain	Residue
A	CYS238
A	HIS244
A	CYS310
A	CYS312

---

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI A 1339

Chain	Residue
A	HIS192
A	GLU194
A	HIS280
A	OGA1341
A	HOH2273

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMD A 1340

Chain	Residue
A	TYR277
A	MET306
A	HOH2282
A	HOH2304

---

site_id	AC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE OGA A 1341

Chain	Residue
A	TYR136
A	PHE189
A	HIS192
A	GLU194
A	SER200
A	ASN202
A	LYS210
A	HIS280
A	ALA292
A	NI1339
A	EDO1343
A	HOH2273
A	HOH2384

---

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 1342

Chain	Residue
A	ASN106
A	HOH2108

---

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 1343

Chain	Residue
A	TYR179
A	TYR181
A	GLU194
A	ALA292
A	ASN294
A	OGA1341
A	HOH2273

---

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 1344

Chain	Residue
A	LYS150
A	GLN151
A	TRP152
A	ASN153
A	HIS156
A	HOH2049
A	HOH2050

---

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 1345

Chain	Residue
A	GLU39
A	THR297
A	PRO298
A	ARG299
A	HOH2061
A	HOH2385

---

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 1346

Chain	Residue
A	SER80
A	THR87
A	PHE231
A	LYS305
A	HOH2265
A	HOH2314

---

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 1347

Chain	Residue
A	MET19
A	ILE20
A	HOH2021
A	HOH2386

---

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 1348

Chain	Residue
A	SER143
A	THR159
A	GLN161
A	ASP162
A	GLY174
A	VAL175
A	EDO1350
A	HOH2233

---

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 1349

Chain	Residue
A	GLY84
A	TRP126
A	SER250
A	HOH2218
A	HOH2333
A	HOH2388

---

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 1350

Chain	Residue
A	PHE145
A	ASP146
A	GLU147
A	ASN153
A	HIS156
A	ASP162
A	EDO1348
A	HOH2257

---

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 1351

Chain	Residue
A	PHE118
A	GLU122
A	ARG263
A	ILE264
A	THR265
A	HOH2389

---

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DMS A 1352

Chain	Residue
A	PRO113
A	LYS124
A	ASN128
A	TRP185
A	LYS186

---

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 1353

Chain	Residue
A	LYS124
A	LYS127
A	ASN128

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	42
Details	Domain: {"description":"JmjN","evidences":[{"source":"PROSITE-ProRule","id":"PRU00537","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	166
Details	Domain: {"description":"JmjC","evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"B2RXH2","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PDB","id":"5F5A","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F5C","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"PolyADP-ribosyl glutamic acid","evidences":[{"source":"PubMed","id":"23102699","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---