Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3W0T

Human Glyoxalase I with an N-hydroxypyridone derivative inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004462	molecular_function	lactoylglutathione lyase activity
A	0005515	molecular_function	protein binding
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0005975	biological_process	carbohydrate metabolic process
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0006749	biological_process	glutathione metabolic process
A	0008270	molecular_function	zinc ion binding
A	0009438	biological_process	methylglyoxal metabolic process
A	0016829	molecular_function	lyase activity
A	0030316	biological_process	osteoclast differentiation
A	0043066	biological_process	negative regulation of apoptotic process
A	0046872	molecular_function	metal ion binding
A	0070062	cellular_component	extracellular exosome
B	0004462	molecular_function	lactoylglutathione lyase activity
B	0005515	molecular_function	protein binding
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0005975	biological_process	carbohydrate metabolic process
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0006749	biological_process	glutathione metabolic process
B	0008270	molecular_function	zinc ion binding
B	0009438	biological_process	methylglyoxal metabolic process
B	0016829	molecular_function	lyase activity
B	0030316	biological_process	osteoclast differentiation
B	0043066	biological_process	negative regulation of apoptotic process
B	0046872	molecular_function	metal ion binding
B	0070062	cellular_component	extracellular exosome
C	0004462	molecular_function	lactoylglutathione lyase activity
C	0005515	molecular_function	protein binding
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0005975	biological_process	carbohydrate metabolic process
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0006749	biological_process	glutathione metabolic process
C	0008270	molecular_function	zinc ion binding
C	0009438	biological_process	methylglyoxal metabolic process
C	0016829	molecular_function	lyase activity
C	0030316	biological_process	osteoclast differentiation
C	0043066	biological_process	negative regulation of apoptotic process
C	0046872	molecular_function	metal ion binding
C	0070062	cellular_component	extracellular exosome
D	0004462	molecular_function	lactoylglutathione lyase activity
D	0005515	molecular_function	protein binding
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0005975	biological_process	carbohydrate metabolic process
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0006749	biological_process	glutathione metabolic process
D	0008270	molecular_function	zinc ion binding
D	0009438	biological_process	methylglyoxal metabolic process
D	0016829	molecular_function	lyase activity
D	0030316	biological_process	osteoclast differentiation
D	0043066	biological_process	negative regulation of apoptotic process
D	0046872	molecular_function	metal ion binding
D	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 201

Chain	Residue
A	GLN33
A	GLU99
B	HIS126
B	GLU172
B	HPU204

site_id	AC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE HPU A 202

Chain	Residue
A	HOH473
B	GLN33
B	MET35
B	CYS60
B	PHE67
B	LEU69
B	LEU92
B	GLU99
B	ZN201
B	HOH1024
B	HOH1048
A	HIS126
A	MET157
A	GLU172
A	MET179

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 201

Chain	Residue
A	HIS126
A	GLU172
A	HPU202
B	GLN33
B	GLU99

site_id	AC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE EPE B 202

Chain	Residue
A	MET65
B	LYS150
B	GLY155
B	LYS156
B	MET157
B	HPU204
B	HOH1197
B	HOH1213
D	GLU110
D	HOH526
D	HOH546

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EPE B 203

Chain	Residue
B	SER20
B	ASP21
B	HOH1196

site_id	AC6
Number of Residues	18
Details	BINDING SITE FOR RESIDUE HPU B 204

Chain	Residue
A	GLN33
A	MET35
A	CYS60
A	PHE67
A	LEU69
A	GLU99
A	ZN201
A	HOH337
B	HIS126
B	MET157
B	LEU160
B	GLU172
B	MET179
B	MET183
B	EPE202
B	HOH1065
B	HOH1154
B	HOH1197

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 201

Chain	Residue
C	GLN33
C	GLU99
D	HIS126
D	GLU172
D	HPU203

site_id	AC8
Number of Residues	15
Details	BINDING SITE FOR RESIDUE HPU C 202

Chain	Residue
C	HIS126
C	GLU172
C	MET179
C	MET183
C	HOH450
C	HOH468
D	GLN33
D	MET35
D	CYS60
D	PHE67
D	LEU69
D	GLU99
D	ZN201
D	HOH325
D	HOH335

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 201

Chain	Residue
C	HIS126
C	GLU172
C	HPU202
D	GLN33
D	GLU99

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EPE D 202

Chain	Residue
B	GLU83
D	CYS19
D	SER20
D	ASP21
D	HOH472

site_id	BC2
Number of Residues	16
Details	BINDING SITE FOR RESIDUE HPU D 203

Chain	Residue
D	GLU172
D	MET179
D	MET183
D	HOH374
B	GLU2
B	PRO3
C	GLN33
C	MET35
C	CYS60
C	PHE62
C	LEU69
C	PHE71
C	GLU99
C	ZN201
C	HOH327
D	HIS126

Functional Information from PROSITE/UniProt

site_id	PS00934
Number of Residues	22
Details	GLYOXALASE_I_1 Glyoxalase I signature 1. QTmLrVkdpkKSldFYtrvLGM

Chain	Residue	Details
A	GLN33-MET54

site_id	PS00935
Number of Residues	17
Details	GLYOXALASE_I_2 Glyoxalase I signature 2. GNsdpr.GFGHIGiAvpD

Chain	Residue	Details
A	GLY117-ASP133

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Proton donor/acceptor => ECO:0000269\|PubMed:10521255, ECO:0000269\|PubMed:9705294

Chain	Residue	Details
A	GLU172
B	GLU172
C	GLU172
D	GLU172

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:23122816, ECO:0000269\|PubMed:9218781, ECO:0000269\|PubMed:9705294

Chain	Residue	Details
A	GLN33
A	GLU99
B	GLN33
B	GLU99
C	GLN33
C	GLU99
D	GLN33
D	GLU99

site_id	SWS_FT_FI3
Number of Residues	8
Details	BINDING:

Chain	Residue	Details
A	ARG37
A	ASN103
B	ARG37
B	ASN103
C	ARG37
C	ASN103
D	ARG37
D	ASN103

site_id	SWS_FT_FI4
Number of Residues	8
Details	BINDING: in other chain

Chain	Residue	Details
A	ARG122
A	LYS156
B	ARG122
B	LYS156
C	ARG122
C	LYS156
D	ARG122
D	LYS156

site_id	SWS_FT_FI5
Number of Residues	8
Details	BINDING: in other chain => ECO:0000269\|PubMed:23122816, ECO:0000269\|PubMed:9218781, ECO:0000269\|PubMed:9705294

Chain	Residue	Details
A	HIS126
A	GLU172
B	HIS126
B	GLU172
C	HIS126
C	GLU172
D	HIS126
D	GLU172

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: N-acetylalanine => ECO:0000269\|PubMed:20454679, ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:25944712

Chain	Residue	Details
A	ALA1
B	ALA1
C	ALA1
D	ALA1

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: N6-succinyllysine => ECO:0000250\|UniProtKB:Q9CPU0

Chain	Residue	Details
A	LYS87
B	LYS87
C	LYS87
D	LYS87

site_id	SWS_FT_FI8
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269\|PubMed:19199007

Chain	Residue	Details
A	THR106
B	THR106
C	THR106
D	THR106

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: S-glutathionyl cysteine; alternate => ECO:0000269\|PubMed:20454679

Chain	Residue	Details
A	CYS138
B	CYS138
C	CYS138
D	CYS138

site_id	SWS_FT_FI10
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:Q9CPU0

Chain	Residue	Details
A	LYS147
B	LYS147
C	LYS147
D	LYS147

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 32

Chain	Residue	Details
A	GLN33	metal ligand
A	GLU99	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
A	HIS126	metal ligand
A	GLU172	hydrogen bond acceptor, metal ligand, proton acceptor, proton donor, proton relay

site_id	MCSA2
Number of Residues	4
Details	M-CSA 32

Chain	Residue	Details
B	GLN33	metal ligand
B	GLU99	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
B	HIS126	metal ligand
B	GLU172	hydrogen bond acceptor, metal ligand, proton acceptor, proton donor, proton relay

site_id	MCSA3
Number of Residues	4
Details	M-CSA 32

Chain	Residue	Details
C	GLN33	metal ligand
C	GLU99	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
C	HIS126	metal ligand
C	GLU172	hydrogen bond acceptor, metal ligand, proton acceptor, proton donor, proton relay

site_id	MCSA4
Number of Residues	4
Details	M-CSA 32

Chain	Residue	Details
D	GLN33	metal ligand
D	GLU99	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
D	HIS126	metal ligand
D	GLU172	hydrogen bond acceptor, metal ligand, proton acceptor, proton donor, proton relay

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