4L06

Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005777	cellular_component	peroxisome
A	0005782	cellular_component	peroxisomal matrix
A	0005829	cellular_component	cytosol
A	0006097	biological_process	glyoxylate cycle
A	0006099	biological_process	tricarboxylic acid cycle
A	0006102	biological_process	isocitrate metabolic process
A	0006103	biological_process	2-oxoglutarate metabolic process
A	0006739	biological_process	NADP metabolic process
A	0006749	biological_process	glutathione metabolic process
A	0006979	biological_process	response to oxidative stress
A	0008585	biological_process	female gonad development
A	0014070	biological_process	response to organic cyclic compound
A	0016491	molecular_function	oxidoreductase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0034774	cellular_component	secretory granule lumen
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0045296	molecular_function	cadherin binding
A	0046872	molecular_function	metal ion binding
A	0048545	biological_process	response to steroid hormone
A	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
A	0060696	biological_process	regulation of phospholipid catabolic process
A	0070062	cellular_component	extracellular exosome
A	0071071	biological_process	regulation of phospholipid biosynthetic process
A	1904724	cellular_component	tertiary granule lumen
A	1904813	cellular_component	ficolin-1-rich granule lumen
B	0000287	molecular_function	magnesium ion binding
B	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005777	cellular_component	peroxisome
B	0005782	cellular_component	peroxisomal matrix
B	0005829	cellular_component	cytosol
B	0006097	biological_process	glyoxylate cycle
B	0006099	biological_process	tricarboxylic acid cycle
B	0006102	biological_process	isocitrate metabolic process
B	0006103	biological_process	2-oxoglutarate metabolic process
B	0006739	biological_process	NADP metabolic process
B	0006749	biological_process	glutathione metabolic process
B	0006979	biological_process	response to oxidative stress
B	0008585	biological_process	female gonad development
B	0014070	biological_process	response to organic cyclic compound
B	0016491	molecular_function	oxidoreductase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0034774	cellular_component	secretory granule lumen
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0045296	molecular_function	cadherin binding
B	0046872	molecular_function	metal ion binding
B	0048545	biological_process	response to steroid hormone
B	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
B	0060696	biological_process	regulation of phospholipid catabolic process
B	0070062	cellular_component	extracellular exosome
B	0071071	biological_process	regulation of phospholipid biosynthetic process
B	1904724	cellular_component	tertiary granule lumen
B	1904813	cellular_component	ficolin-1-rich granule lumen
C	0000287	molecular_function	magnesium ion binding
C	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
C	0005515	molecular_function	protein binding
C	0005576	cellular_component	extracellular region
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005777	cellular_component	peroxisome
C	0005782	cellular_component	peroxisomal matrix
C	0005829	cellular_component	cytosol
C	0006097	biological_process	glyoxylate cycle
C	0006099	biological_process	tricarboxylic acid cycle
C	0006102	biological_process	isocitrate metabolic process
C	0006103	biological_process	2-oxoglutarate metabolic process
C	0006739	biological_process	NADP metabolic process
C	0006749	biological_process	glutathione metabolic process
C	0006979	biological_process	response to oxidative stress
C	0008585	biological_process	female gonad development
C	0014070	biological_process	response to organic cyclic compound
C	0016491	molecular_function	oxidoreductase activity
C	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C	0034774	cellular_component	secretory granule lumen
C	0042802	molecular_function	identical protein binding
C	0042803	molecular_function	protein homodimerization activity
C	0045296	molecular_function	cadherin binding
C	0046872	molecular_function	metal ion binding
C	0048545	biological_process	response to steroid hormone
C	0050661	molecular_function	NADP binding
C	0051287	molecular_function	NAD binding
C	0060696	biological_process	regulation of phospholipid catabolic process
C	0070062	cellular_component	extracellular exosome
C	0071071	biological_process	regulation of phospholipid biosynthetic process
C	1904724	cellular_component	tertiary granule lumen
C	1904813	cellular_component	ficolin-1-rich granule lumen
D	0000287	molecular_function	magnesium ion binding
D	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
D	0005515	molecular_function	protein binding
D	0005576	cellular_component	extracellular region
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005777	cellular_component	peroxisome
D	0005782	cellular_component	peroxisomal matrix
D	0005829	cellular_component	cytosol
D	0006097	biological_process	glyoxylate cycle
D	0006099	biological_process	tricarboxylic acid cycle
D	0006102	biological_process	isocitrate metabolic process
D	0006103	biological_process	2-oxoglutarate metabolic process
D	0006739	biological_process	NADP metabolic process
D	0006749	biological_process	glutathione metabolic process
D	0006979	biological_process	response to oxidative stress
D	0008585	biological_process	female gonad development
D	0014070	biological_process	response to organic cyclic compound
D	0016491	molecular_function	oxidoreductase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0034774	cellular_component	secretory granule lumen
D	0042802	molecular_function	identical protein binding
D	0042803	molecular_function	protein homodimerization activity
D	0045296	molecular_function	cadherin binding
D	0046872	molecular_function	metal ion binding
D	0048545	biological_process	response to steroid hormone
D	0050661	molecular_function	NADP binding
D	0051287	molecular_function	NAD binding
D	0060696	biological_process	regulation of phospholipid catabolic process
D	0070062	cellular_component	extracellular exosome
D	0071071	biological_process	regulation of phospholipid biosynthetic process
D	1904724	cellular_component	tertiary granule lumen
D	1904813	cellular_component	ficolin-1-rich granule lumen
E	0000287	molecular_function	magnesium ion binding
E	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
E	0005515	molecular_function	protein binding
E	0005576	cellular_component	extracellular region
E	0005737	cellular_component	cytoplasm
E	0005739	cellular_component	mitochondrion
E	0005777	cellular_component	peroxisome
E	0005782	cellular_component	peroxisomal matrix
E	0005829	cellular_component	cytosol
E	0006097	biological_process	glyoxylate cycle
E	0006099	biological_process	tricarboxylic acid cycle
E	0006102	biological_process	isocitrate metabolic process
E	0006103	biological_process	2-oxoglutarate metabolic process
E	0006739	biological_process	NADP metabolic process
E	0006749	biological_process	glutathione metabolic process
E	0006979	biological_process	response to oxidative stress
E	0008585	biological_process	female gonad development
E	0014070	biological_process	response to organic cyclic compound
E	0016491	molecular_function	oxidoreductase activity
E	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E	0034774	cellular_component	secretory granule lumen
E	0042802	molecular_function	identical protein binding
E	0042803	molecular_function	protein homodimerization activity
E	0045296	molecular_function	cadherin binding
E	0046872	molecular_function	metal ion binding
E	0048545	biological_process	response to steroid hormone
E	0050661	molecular_function	NADP binding
E	0051287	molecular_function	NAD binding
E	0060696	biological_process	regulation of phospholipid catabolic process
E	0070062	cellular_component	extracellular exosome
E	0071071	biological_process	regulation of phospholipid biosynthetic process
E	1904724	cellular_component	tertiary granule lumen
E	1904813	cellular_component	ficolin-1-rich granule lumen
F	0000287	molecular_function	magnesium ion binding
F	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
F	0005515	molecular_function	protein binding
F	0005576	cellular_component	extracellular region
F	0005737	cellular_component	cytoplasm
F	0005739	cellular_component	mitochondrion
F	0005777	cellular_component	peroxisome
F	0005782	cellular_component	peroxisomal matrix
F	0005829	cellular_component	cytosol
F	0006097	biological_process	glyoxylate cycle
F	0006099	biological_process	tricarboxylic acid cycle
F	0006102	biological_process	isocitrate metabolic process
F	0006103	biological_process	2-oxoglutarate metabolic process
F	0006739	biological_process	NADP metabolic process
F	0006749	biological_process	glutathione metabolic process
F	0006979	biological_process	response to oxidative stress
F	0008585	biological_process	female gonad development
F	0014070	biological_process	response to organic cyclic compound
F	0016491	molecular_function	oxidoreductase activity
F	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F	0034774	cellular_component	secretory granule lumen
F	0042802	molecular_function	identical protein binding
F	0042803	molecular_function	protein homodimerization activity
F	0045296	molecular_function	cadherin binding
F	0046872	molecular_function	metal ion binding
F	0048545	biological_process	response to steroid hormone
F	0050661	molecular_function	NADP binding
F	0051287	molecular_function	NAD binding
F	0060696	biological_process	regulation of phospholipid catabolic process
F	0070062	cellular_component	extracellular exosome
F	0071071	biological_process	regulation of phospholipid biosynthetic process
F	1904724	cellular_component	tertiary granule lumen
F	1904813	cellular_component	ficolin-1-rich granule lumen

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA A 501

Chain	Residue
A	ASP275
A	ASP279
A	AKG503
B	ASP252

---

site_id	AC2
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAP A 502

Chain	Residue
A	ARG82
A	ASN96
A	LEU288
A	ALA307
A	HIS309
A	GLY310
A	THR311
A	VAL312
A	THR313
A	ARG314
A	HIS315
A	ASN328
A	AKG503
A	HOH607
A	HOH608
A	HOH609
A	HOH610
A	HOH640
A	HOH641
B	LEU250
B	ASP253
B	GLN257
B	LYS260
A	LYS72
A	ALA74
A	THR75
A	ILE76
A	THR77

---

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AKG A 503

Chain	Residue
A	THR77
A	SER94
A	ASN96
A	ARG100
A	ARG109
A	ARG132
A	ASP275
A	CA501
A	NAP502
A	HOH607
A	HOH627
B	ASP252

---

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA B 501

Chain	Residue
A	ASP252
B	ASP275
B	ASP279
B	AKG503

---

site_id	AC5
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAP B 502

Chain	Residue
A	LEU250
A	ASP253
A	GLN257
A	LYS260
B	LYS72
B	ALA74
B	THR75
B	THR77
B	ARG82
B	ASN96
B	LEU288
B	ALA307
B	HIS309
B	GLY310
B	THR311
B	VAL312
B	ARG314
B	HIS315
B	THR327
B	ASN328
B	AKG503
B	HOH613
B	HOH614

---

site_id	AC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AKG B 503

Chain	Residue
A	ASP252
B	THR77
B	SER94
B	ASN96
B	ARG100
B	ARG109
B	ARG132
B	ASP275
B	ALA308
B	CA501
B	NAP502

---

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA C 501

Chain	Residue
C	ASP275
C	ASP279
C	AKG503
C	HOH610
D	ASP252

---

site_id	AC8
Number of Residues	24
Details	BINDING SITE FOR RESIDUE NAP C 502

Chain	Residue
C	VAL312
C	THR313
C	ARG314
C	HIS315
C	ASN328
C	AKG503
C	HOH604
C	HOH614
D	LEU250
D	ASP253
D	GLN257
D	LYS260
C	LYS72
C	ALA74
C	THR75
C	ILE76
C	THR77
C	ARG82
C	ASN96
C	ALA307
C	ALA308
C	HIS309
C	GLY310
C	THR311

---

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE AKG C 503

Chain	Residue
C	THR77
C	SER94
C	ASN96
C	ARG100
C	ARG109
C	ARG132
C	ASP275
C	ALA308
C	CA501
C	NAP502
D	LYS212
D	ILE215
D	ASP252

---

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA D 501

Chain	Residue
C	ASP252
D	ARG109
D	ASP275
D	ASP279
D	AKG503

---

site_id	BC2
Number of Residues	19
Details	BINDING SITE FOR RESIDUE NAP D 502

Chain	Residue
C	ASP253
C	GLN257
C	LYS260
D	LYS72
D	ALA74
D	THR75
D	THR77
D	ARG82
D	ASN96
D	ALA307
D	ALA308
D	HIS309
D	GLY310
D	THR311
D	VAL312
D	ARG314
D	HIS315
D	ASN328
D	AKG503

---

site_id	BC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AKG D 503

Chain	Residue
C	ASP252
D	THR77
D	SER94
D	ASN96
D	ARG100
D	ARG109
D	ARG132
D	ASP275
D	ALA308
D	CA501
D	NAP502

---

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA E 501

Chain	Residue
E	ASP275
E	ASP279
E	AKG503
E	HOH624
F	ASP252

---

site_id	BC5
Number of Residues	25
Details	BINDING SITE FOR RESIDUE NAP E 502

Chain	Residue
E	LYS72
E	ALA74
E	THR75
E	ILE76
E	THR77
E	ARG82
E	ASN96
E	LEU288
E	ALA307
E	HIS309
E	GLY310
E	THR311
E	VAL312
E	THR313
E	ARG314
E	HIS315
E	THR327
E	ASN328
E	AKG503
E	HOH610
E	HOH618
F	LEU250
F	ASP253
F	GLN257
F	LYS260

---

site_id	BC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AKG E 503

Chain	Residue
E	THR77
E	SER94
E	ASN96
E	ARG100
E	ARG109
E	ARG132
E	ASP275
E	ALA308
E	CA501
E	NAP502
F	LYS212
F	ASP252

---

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA F 501

Chain	Residue
E	ASP252
F	ASP275
F	ASP279
F	AKG503

---

site_id	BC8
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAP F 502

Chain	Residue
E	LEU250
E	ASP253
E	GLN257
E	LYS260
F	LYS72
F	ALA74
F	THR75
F	ILE76
F	THR77
F	ARG82
F	ASN96
F	ALA307
F	HIS309
F	GLY310
F	THR311
F	VAL312
F	THR313
F	ARG314
F	HIS315
F	ASN328
F	AKG503
F	HOH602
F	HOH609

---

site_id	BC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AKG F 503

Chain	Residue
E	ASP252
F	THR77
F	SER94
F	ASN96
F	ARG100
F	ARG109
F	ARG132
F	ASP275
F	ALA308
F	CA501
F	NAP502

---

Functional Information from PROSITE/UniProt

site_id	PS00470
Number of Residues	20
Details	IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NYDGDVqSDsvAqgy.GSLGM

Chain	Residue	Details
A	ASN271-MET290

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	18
Details	BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T09, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM, ECO:0007744|PDB:3MAP, ECO:0007744|PDB:3MAR, ECO:0007744|PDB:3MAS, ECO:0007744|PDB:4I3K, ECO:0007744|PDB:4I3L, ECO:0007744|PDB:4KZO, ECO:0007744|PDB:4L03, ECO:0007744|PDB:4L04, ECO:0007744|PDB:4L06, ECO:0007744|PDB:4UMX, ECO:0007744|PDB:4UMY, ECO:0007744|PDB:4XRX, ECO:0007744|PDB:4XS3, ECO:0007744|PDB:5DE1, ECO:0007744|PDB:5L57, ECO:0007744|PDB:5L58, ECO:0007744|PDB:5LGE, ECO:0007744|PDB:5SUN, ECO:0007744|PDB:5SVF, ECO:0007744|PDB:5TQH

Chain	Residue	Details
A	THR75
D	THR75
D	GLY310
D	ASN328
E	THR75
E	GLY310
E	ASN328
F	THR75
F	GLY310
F	ASN328
A	GLY310
A	ASN328
B	THR75
B	GLY310
B	ASN328
C	THR75
C	GLY310
C	ASN328

---

site_id	SWS_FT_FI2
Number of Residues	24
Details	BINDING: in other chain => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L

Chain	Residue	Details
A	THR77
C	SER94
C	ARG109
C	ARG132
D	THR77
D	SER94
D	ARG109
D	ARG132
E	THR77
E	SER94
E	ARG109
A	SER94
E	ARG132
F	THR77
F	SER94
F	ARG109
F	ARG132
A	ARG109
A	ARG132
B	THR77
B	SER94
B	ARG109
B	ARG132
C	THR77

---

site_id	SWS_FT_FI3
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T09, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM, ECO:0007744|PDB:3MAP, ECO:0007744|PDB:3MAR, ECO:0007744|PDB:3MAS, ECO:0007744|PDB:4I3K, ECO:0007744|PDB:4I3L, ECO:0007744|PDB:4KZO, ECO:0007744|PDB:4L03, ECO:0007744|PDB:4L04, ECO:0007744|PDB:4L06, ECO:0007744|PDB:4UMX, ECO:0007744|PDB:4UMY, ECO:0007744|PDB:4XRX, ECO:0007744|PDB:4XS3, ECO:0007744|PDB:5DE1, ECO:0007744|PDB:5L57, ECO:0007744|PDB:5LGE, ECO:0007744|PDB:5SUN, ECO:0007744|PDB:5SVF, ECO:0007744|PDB:5TQH

Chain	Residue	Details
A	ARG82
B	ARG82
C	ARG82
D	ARG82
E	ARG82
F	ARG82

---

site_id	SWS_FT_FI4
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0007744|PDB:1T0L

Chain	Residue	Details
A	LYS212
B	LYS212
C	LYS212
D	LYS212
E	LYS212
F	LYS212

---

site_id	SWS_FT_FI5
Number of Residues	6
Details	BINDING: BINDING => ECO:0000305|PubMed:15173171, ECO:0000305|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM

Chain	Residue	Details
A	ASP252
B	ASP252
C	ASP252
D	ASP252
E	ASP252
F	ASP252

---

site_id	SWS_FT_FI6
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269|PubMed:15173171, ECO:0000269|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM

Chain	Residue	Details
A	LYS260
B	LYS260
C	LYS260
D	LYS260
E	LYS260
F	LYS260

---

site_id	SWS_FT_FI7
Number of Residues	12
Details	BINDING: in other chain => ECO:0000305|PubMed:15173171, ECO:0000305|PubMed:19935646, ECO:0007744|PDB:1T0L, ECO:0007744|PDB:3INM

Chain	Residue	Details
A	ASP275
E	ASP279
F	ASP275
F	ASP279
A	ASP279
B	ASP275
B	ASP279
C	ASP275
C	ASP279
D	ASP275
D	ASP279
E	ASP275

---

site_id	SWS_FT_FI8
Number of Residues	12
Details	SITE: Critical for catalysis

Chain	Residue	Details
A	ASP139
E	LYS212
F	ASP139
F	LYS212
A	LYS212
B	ASP139
B	LYS212
C	ASP139
C	LYS212
D	ASP139
D	LYS212
E	ASP139

---

site_id	SWS_FT_FI9
Number of Residues	6
Details	MOD_RES: N-acetylserine => ECO:0007744|PubMed:22814378

Chain	Residue	Details
A	SER2
B	SER2
C	SER2
D	SER2
E	SER2
F	SER2

---

site_id	SWS_FT_FI10
Number of Residues	6
Details	MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
A	TYR42
B	TYR42
C	TYR42
D	TYR42
E	TYR42
F	TYR42

---

site_id	SWS_FT_FI11
Number of Residues	24
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O88844

Chain	Residue	Details
A	LYS81
C	LYS224
C	LYS233
C	LYS243
D	LYS81
D	LYS224
D	LYS233
D	LYS243
E	LYS81
E	LYS224
E	LYS233
A	LYS224
E	LYS243
F	LYS81
F	LYS224
F	LYS233
F	LYS243
A	LYS233
A	LYS243
B	LYS81
B	LYS224
B	LYS233
B	LYS243
C	LYS81

---

site_id	SWS_FT_FI12
Number of Residues	12
Details	MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:O88844

Chain	Residue	Details
A	LYS126
E	LYS400
F	LYS126
F	LYS400
A	LYS400
B	LYS126
B	LYS400
C	LYS126
C	LYS400
D	LYS126
D	LYS400
E	LYS126

---

site_id	SWS_FT_FI13
Number of Residues	6
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
A	LYS321
B	LYS321
C	LYS321
D	LYS321
E	LYS321
F	LYS321

---

site_id	SWS_FT_FI14
Number of Residues	6
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O88844

Chain	Residue	Details
A	SER389
B	SER389
C	SER389
D	SER389
E	SER389
F	SER389

---