Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6VB9

Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lyase-1 from Mycobacterium tuberculosis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004451	molecular_function	isocitrate lyase activity
A	0005576	cellular_component	extracellular region
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006097	biological_process	glyoxylate cycle
A	0006099	biological_process	tricarboxylic acid cycle
A	0006102	biological_process	isocitrate metabolic process
A	0016829	molecular_function	lyase activity
A	0019752	biological_process	carboxylic acid metabolic process
A	0035375	molecular_function	zymogen binding
A	0046421	molecular_function	methylisocitrate lyase activity
A	0046872	molecular_function	metal ion binding
A	0071456	biological_process	cellular response to hypoxia
B	0003824	molecular_function	catalytic activity
B	0004451	molecular_function	isocitrate lyase activity
B	0005576	cellular_component	extracellular region
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0006097	biological_process	glyoxylate cycle
B	0006099	biological_process	tricarboxylic acid cycle
B	0006102	biological_process	isocitrate metabolic process
B	0016829	molecular_function	lyase activity
B	0019752	biological_process	carboxylic acid metabolic process
B	0035375	molecular_function	zymogen binding
B	0046421	molecular_function	methylisocitrate lyase activity
B	0046872	molecular_function	metal ion binding
B	0071456	biological_process	cellular response to hypoxia
C	0003824	molecular_function	catalytic activity
C	0004451	molecular_function	isocitrate lyase activity
C	0005576	cellular_component	extracellular region
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006097	biological_process	glyoxylate cycle
C	0006099	biological_process	tricarboxylic acid cycle
C	0006102	biological_process	isocitrate metabolic process
C	0016829	molecular_function	lyase activity
C	0019752	biological_process	carboxylic acid metabolic process
C	0035375	molecular_function	zymogen binding
C	0046421	molecular_function	methylisocitrate lyase activity
C	0046872	molecular_function	metal ion binding
C	0071456	biological_process	cellular response to hypoxia
D	0003824	molecular_function	catalytic activity
D	0004451	molecular_function	isocitrate lyase activity
D	0005576	cellular_component	extracellular region
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006097	biological_process	glyoxylate cycle
D	0006099	biological_process	tricarboxylic acid cycle
D	0006102	biological_process	isocitrate metabolic process
D	0016829	molecular_function	lyase activity
D	0019752	biological_process	carboxylic acid metabolic process
D	0035375	molecular_function	zymogen binding
D	0046421	molecular_function	methylisocitrate lyase activity
D	0046872	molecular_function	metal ion binding
D	0071456	biological_process	cellular response to hypoxia

Functional Information from PDB Data

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

Chain	Residue
A	ASP153
A	OXD503
A	HOH606
A	HOH622
A	HOH643

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 502

Chain	Residue
A	HOH818
A	HOH827
A	ALA276
A	ALA279
A	GLN308
A	HOH765

site_id	AC3
Number of Residues	14
Details	binding site for residue OXD A 503

Chain	Residue
A	TYR89
A	SER91
A	GLY92
A	TRP93
A	ASP153
A	HIS180
A	QVA191
A	ARG228
A	TRP283
A	THR347
A	MG501
A	HOH606
A	HOH622
A	HOH643

site_id	AC4
Number of Residues	3
Details	binding site for residue ACY A 504

Chain	Residue
A	TRP65
A	HOH624
B	HOH654

site_id	AC5
Number of Residues	3
Details	binding site for residue ACY A 505

Chain	Residue
A	PRO21
A	TRP57
A	GLU58

site_id	AC6
Number of Residues	5
Details	binding site for residue MG B 501

Chain	Residue
B	ASP153
B	OXD503
B	HOH602
B	HOH619
B	HOH645

site_id	AC7
Number of Residues	6
Details	binding site for residue PEG B 502

Chain	Residue
B	LEU185
B	GLN204
B	THR238
B	HOH813
C	LEU185
C	SER187

site_id	AC8
Number of Residues	13
Details	binding site for residue OXD B 503

Chain	Residue
B	TYR89
B	SER91
B	GLY92
B	TRP93
B	ASP153
B	HIS180
B	QVA191
B	ARG228
B	TRP283
B	THR347
B	MG501
B	HOH602
B	HOH645

site_id	AC9
Number of Residues	4
Details	binding site for residue ACY B 504

Chain	Residue
B	TRP17
B	TRP23
B	ARG28
B	ASP217

site_id	AD1
Number of Residues	3
Details	binding site for residue ACY B 505

Chain	Residue
B	GLN204
B	ARG207
D	ASP410

site_id	AD2
Number of Residues	1
Details	binding site for residue ACY B 506

Chain	Residue
B	TRP65

site_id	AD3
Number of Residues	5
Details	binding site for residue MG C 501

Chain	Residue
C	ASP153
C	OXD504
C	HOH614
C	HOH628
C	HOH640

site_id	AD4
Number of Residues	6
Details	binding site for residue MG C 502

Chain	Residue
C	ALA276
C	ALA279
C	GLN308
C	HOH636
C	HOH800
C	HOH814

site_id	AD5
Number of Residues	12
Details	binding site for residue PEG C 503

Chain	Residue
C	VAL78
C	GLN79
C	ARG82
C	ALA131
C	ILE134
C	ALA135
C	TRP146
C	THR389
C	ARG395
C	GLU396
C	HOH607
C	HOH647

site_id	AD6
Number of Residues	14
Details	binding site for residue OXD C 504

Chain	Residue
C	HOH640
C	TYR89
C	SER91
C	GLY92
C	TRP93
C	ASP153
C	HIS180
C	QVA191
C	ARG228
C	TRP283
C	THR347
C	MG501
C	HOH614
C	HOH628

site_id	AD7
Number of Residues	2
Details	binding site for residue ACY C 505

Chain	Residue
C	TRP65
C	ASN67

site_id	AD8
Number of Residues	6
Details	binding site for residue MG D 501

Chain	Residue
D	ALA276
D	ALA279
D	GLN308
D	HOH730
D	HOH738
D	HOH796

site_id	AD9
Number of Residues	5
Details	binding site for residue MG D 502

Chain	Residue
D	ASP153
D	OXD503
D	HOH605
D	HOH620
D	HOH633

site_id	AE1
Number of Residues	12
Details	binding site for residue OXD D 503

Chain	Residue
D	TYR89
D	SER91
D	GLY92
D	TRP93
D	ASP153
D	HIS180
D	QVA191
D	ARG228
D	THR347
D	MG502
D	HOH620
D	HOH633

site_id	AE2
Number of Residues	5
Details	binding site for residue ACY D 504

Chain	Residue
D	TRP17
D	TRP23
D	ASP217
D	ASP220
D	VAL221

site_id	AE3
Number of Residues	5
Details	binding site for residue ACY D 505

Chain	Residue
D	PRO7
D	LYS8
D	ILE13
D	GLN39
D	ASP220

site_id	AE4
Number of Residues	2
Details	binding site for residue ACY D 506

Chain	Residue
D	GLU64
D	TRP65

Functional Information from PROSITE/UniProt

site_id	PS00161
Number of Residues	6
Details	ISOCITRATE_LYASE Isocitrate lyase signature. KKCGHL

Chain	Residue	Details
A	LYS189-LEU194

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"24354272","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	40
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10932251","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Cross-link: {"description":"Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup)","evidences":[{"source":"PubMed","id":"20066036","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
A	ASP153	metal ligand
A	HIS180	electrostatic stabiliser, hydrogen bond donor
A	QVA191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
A	LYS197	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
A	GLU232	electrostatic stabiliser, hydrogen bond donor
A	ASN319	electrostatic stabiliser, hydrogen bond donor
A	LYS321	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA2
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
B	ASP153	metal ligand
B	HIS180	electrostatic stabiliser, hydrogen bond donor
B	QVA191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
B	LYS197	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
B	GLU232	electrostatic stabiliser, hydrogen bond donor
B	ASN319	electrostatic stabiliser, hydrogen bond donor
B	LYS321	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA3
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
C	ASP153	metal ligand
C	HIS180	electrostatic stabiliser, hydrogen bond donor
C	QVA191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
C	LYS197	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
C	GLU232	electrostatic stabiliser, hydrogen bond donor
C	ASN319	electrostatic stabiliser, hydrogen bond donor
C	LYS321	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA4
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
D	ASP153	metal ligand
D	HIS180	electrostatic stabiliser, hydrogen bond donor
D	QVA191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
D	LYS197	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
D	GLU232	electrostatic stabiliser, hydrogen bond donor
D	ASN319	electrostatic stabiliser, hydrogen bond donor
D	LYS321	electrostatic stabiliser, hydrogen bond donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)