Structure for peptidase M28.010: glutamate carboxypeptidase II

Summary Gene structure Alignment Tree Sequences Sequence features Distribution Structure Literature Substrates Pharma

PDB	Organism	Resolution	Comment
1Z8L_A	Homo sapiens	3.50 Å	mature
One molecule of the tetramer is shown. The catalytic zinc ions are shown as light grey CPK spheres. The zinc ligands are shown in ball-and-stick representation: His377 and His553 in purple; Asp387 and Asp453 in pink; and Glu425 in dark blue. The putative catalytic residues are also shown in ball-and-stick representation: Asp379 in pink and Glu424 in dark blue. Carbohydrates are shown as CPK spheres in yellow.

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TERTIARY STRUCTURE DATA
Comment	Resolution	PDB	PDBe	SCOP	CATH	PDBSum	Proteopedia	Reference
Homo sapiens
mature peptidase	3.50 Å	1Z8L	1Z8L	1Z8L	1Z8L	1Z8L	1Z8L	Davis et al., 2005
complex with GPI-18431 (S)-2-(4-iodobenzylphosphonomethyl)-pentanedoic acid	2.00 Å	2C6C	2C6C	2C6C	2C6C	2C6C	2C6C	Mesters et al., 2006
complex with glutamate	2.20 Å	2C6G	2C6G	2C6G	2C6G	2C6G	2C6G	Mesters et al., 2006
complex with phosphate anion	2.39 Å	2C6P	2C6P	2C6P	2C6P	2C6P	2C6P	Mesters et al., 2006
complex with methionine	2.40 Å	2CIJ	2CIJ	2CIJ	2CIJ	2CIJ	2CIJ	Mesters et al., 2006
complex with 2-PMPA (2-phosphonomethyl-pentanedioic acid)	2.19 Å	2JBJ	2JBJ	2JBJ	2JBJ	2JBJ	2JBJ	Mesters et al., 2006
complex with quisqualic acid	2.99 Å	2JBK	2JBK	2JBK	2JBK	2JBK	2JBK	Mesters et al., 2006
mature peptidase	1.64 Å	2OOT	2OOT	2OOT	2OOT	2OOT	2OOT	Barinka et al., 2007
complex with quisqualic acid	1.62 Å	2OR4	2OR4	2OR4	2OR4	2OR4	2OR4	Barinka et al., 2007
complex with L-Ser-O-sulphate	2.11 Å	2PVV	2PVV	2PVV	2PVV	2PVV	2PVV	Barinka et al., 2007
complex with 2-PMPA (2-phosphonomethyl-pentanedioic acid)	1.71 Å	2PVW	2PVW	2PVW	2PVW	2PVW	2PVW	Barinka et al., 2007
complex with antibody-recruiting molecule ARM-P8	1.59 Å	2XEF	2XEF	2XEF	2XEF	2XEF	2XEF	Zhang et al., 2010
human glutamate carboxypeptidase ii in complex with antibody-recruiting molecule arm-p4	1.59 Å	2XEG	2XEG	2XEG	2XEG	2XEG	2XEG
human glutamate carboxypeptidase ii in complex with antibody-recruiting molecule arm-p2	1.69 Å	2XEI	2XEI	2XEI	2XEI	2XEI	2XEI
human glutamate carboxypeptidase ii in complex with arm-m4, urea-based inhibitor	1.78 Å	2XEJ	2XEJ	2XEJ	2XEJ	2XEJ	2XEJ
complex with transition state analogue of Asp-Glu	1.60 Å	3BHX	3BHX	3BHX	3BHX	3BHX	3BHX	Barinka et al., 2008
complex with transition state analogue of Asp-Glu	1.67 Å	3BI0	3BI0	3BI0	3BI0	3BI0	3BI0	Barinka et al., 2008
complex with transition state analogue of methotrexate-lu	1.50 Å	3BI1	3BI1	3BI1	3BI1	3BI1	3BI1	Barinka et al., 2008
Glu424Ala mutant; complex with N-acetyl-Asp-Glu	1.71 Å	3BXM	3BXM	3BXM	3BXM	3BXM	3BXM	Klusak et al., 2009
complex with DCFBD inhibitor	1.69 Å	3D7D	3D7D	3D7D	3D7D	3D7D	3D7D	Barinka et al., 2008
complex with DCIT inhibitor	1.54 Å	3D7F	3D7F	3D7F	3D7F	3D7F	3D7F	Barinka et al., 2008
complex with DCMC inhibitor	1.75 Å	3D7G	3D7G	3D7G	3D7G	3D7G	3D7G	Barinka et al., 2008
complex with DCIBZL inhibitor	1.55 Å	3D7H	3D7H	3D7H	3D7H	3D7H	3D7H	Barinka et al., 2008
complex with dbibzl, a urea-based inhibitor	2.30 Å	3IWW	3IWW	3IWW	3IWW	3IWW	3IWW
N-terminally AviTEV-tagged form; complex with 2-PMPA	1.60 Å	3RBU	3RBU	3RBU	3RBU	3RBU	3RBU	Tykvart et al., 2012
Glu424Ala inactive mutant; complex with n-acetyl-aspartyl-aminononanoic acid	1.70 Å	3SJE	3SJE	3SJE	3SJE	3SJE	3SJE
complex with a urea-based inhibitor (a25)	1.65 Å	3SJF	3SJF	3SJF	3SJF	3SJF	3SJF
human glutamate carboxypeptidase ii (e424a inactive mutant ) in complex with n-acetyl-aspartyl-aminooctanoic acid	1.65 Å	3SJG	3SJG	3SJG	3SJG	3SJG	3SJG
Glu424Ala inactive mutant; complex with n-acetyl-aspartyl-methionine	1.66 Å	3SJX	3SJX	3SJX	3SJX	3SJX	3SJX
complex with ctt1057	1.73 Å	4JYW	4JYW	4JYW	4JYW	4JYW	4JYW
complex with ctt1055	1.83 Å	4JZ0	4JZ0	4JZ0	4JZ0	4JZ0	4JZ0
complex with a phosphoramidate inhibitor ctt1056	1.77 Å	4LQG	4LQG	4LQG	4LQG	4LQG	4LQG
complex with folyl-gamma-l-glutamic acid (pteroyldi-gamma-l-glutamic acid)	1.65 Å	4MCP	4MCP	4MCP	4MCP	4MCP	4MCP
complex with folyldi-gamma-l-glutamic acid (pteroyltri- gamma-l-glutamic acid)	2.00 Å	4MCQ	4MCQ	4MCQ	4MCQ	4MCQ	4MCQ
complex with folyltri-gamma-l-glutamic acid (pteroyltetra-gamma-l-glutamic acid)	1.65 Å	4MCR	4MCR	4MCR	4MCR	4MCR	4MCR
complex with urea-based inhibitor	1.84 Å	4NGM	4NGM	4NGM	4NGM	4NGM	4NGM
complex with urea-based inhibitor	1.64 Å	4NGN	4NGN	4NGN	4NGN	4NGN	4NGN
complex with urea-based inhibitor	1.63 Å	4NGP	4NGP	4NGP	4NGP	4NGP	4NGP
complex with urea-based inhibitor	2.08 Å	4NGQ	4NGQ	4NGQ	4NGQ	4NGQ	4NGQ
complex with urea-based inhibitor	1.90 Å	4NGR	4NGR	4NGR	4NGR	4NGR	4NGR
complex with urea-based inhibitor	1.68 Å	4NGS	4NGS	4NGS	4NGS	4NGS	4NGS
complex with urea-based inhibitor	2.31 Å	4NGT	4NGT	4NGT	4NGT	4NGT	4NGT
complex with ccibzl, a urea-based inhibitor n~2~-[(1- carboxycyclopropyl)carbamoyl]-n~6~-(4-iodobenzoyl)-l-lysine	1.85 Å	4OC0	4OC0	4OC0	4OC0	4OC0	4OC0
complex with coibzl, a urea-based inhibitor (2s)-2-[((1s)-1-carboxy-2-[(2s)-oxiran-2-yl]ethylcarbamoyl)amino]-6-[(4-iodobenzoyl) amino]hexanoic acid	1.75 Å	4OC1	4OC1	4OC1	4OC1	4OC1	4OC1
complex with ceibzl, a urea-based inhibitor n~2~-[(1s)-1-carboxybut-3-yn-1-yl]carbamoyl-n~6~-(4-iodobenzoyl)-l-lysine	1.65 Å	4OC2	4OC2	4OC2	4OC2	4OC2	4OC2
complex with cfibzl, a urea-based inhibitor n~2~-[(1s)-1-carboxy-2- (furan-2-yl)ethyl]carbamoyl-n~6~-(4-iodobenzoyl)-l-lysine	1.79 Å	4OC3	4OC3	4OC3	4OC3	4OC3	4OC3
complex with cpibzl, a urea-based inhibitor n~2~-[(1s)-1-carboxy-2- (pyridin-4-yl)ethyl]carbamoyl-n~6~-(4-iodobenzoyl)-l-lysine	1.66 Å	4OC4	4OC4	4OC4	4OC4	4OC4	4OC4
complex with chibzl, a urea-based inhibitor n~2~-[(s)-carboxy(4- hydroxyphenyl)methyl]carbamoyl-n~6~-(4-iodobenzoyl)-l-lysine	1.70 Å	4OC5	4OC5	4OC5	4OC5	4OC5	4OC5
complex with dccbl, a urea based inhibitor with distal carborane moiety	1.79 Å	4OME	4OME	4OME	4OME	4OME	4OME
complex with a phosphoramidate inhibitor jrb-4-81	1.75 Å	4P44	4P44	4P44	4P44	4P44	4P44
complex with a phosphoramidate inhibitor jrb-4-73	1.87 Å	4P45	4P45	4P45	4P45	4P45	4P45
complex with a phosphoramidate inhibitor ctt54	1.93 Å	4P4B	4P4B	4P4B	4P4B	4P4B	4P4B
complex with a phosphoramidate inhibitor mp1c	1.65 Å	4P4D	4P4D	4P4D	4P4D	4P4D	4P4D
complex with a phosphoramidate inhibitor mp1d	1.67 Å	4P4E	4P4E	4P4E	4P4E	4P4E	4P4E
complex with a phosphoramidate inhibitor nc-2-40	1.86 Å	4P4F	4P4F	4P4F	4P4F	4P4F	4P4F
complex with a phosphoramidate inhibitor t33	1.87 Å	4P4I	4P4I	4P4I	4P4I	4P4I	4P4I
complex with a phosphoramidate inhibitor t33d	1.66 Å	4P4J	4P4J	4P4J	4P4J	4P4J	4P4J
complex with a glutamyl sulfamide inhibitor cjc47	1.64 Å	4W9Y	4W9Y	4W9Y	4W9Y	4W9Y	4W9Y
avi-gcpii structure in complex with fitc-conjugated gcpii-specific inhibitor	1.86 Å	4X3R	4X3R	4X3R	4X3R	4X3R	4X3R
complex with a hydroxamate inhibitor jhu241	1.80 Å	5D29	5D29	5D29	5D29	5D29	5D29
complex with a hydroxamate inhibitor jhu242	1.81 Å	5ELY	5ELY	5ELY	5ELY	5ELY	5ELY
inactive mutant; complex with beta-citryl glutamate	1.85 Å	5F09	5F09	5F09	5F09	5F09	5F09
complex with a urea based inhibitor psma 1023	1.65 Å	5O5R	5O5R	5O5R	5O5R	5O5R	5O5R
complex with a urea based inhibitor psma 1007	1.43 Å	5O5T	5O5T	5O5T	5O5T	5O5T	5O5T
complex with a urea based inhibitor psma 1027	1.53 Å	5O5U	5O5U	5O5U	5O5U	5O5U	5O5U
Glu424Met inactive mutant; complex with a inhibitor cfbzog	1.48 Å	5OF0	5OF0	5OF0	5OF0	5OF0	5OF0
complex with a inhibitor jhu3371	1.68 Å	6ETY	6ETY	6ETY	6ETY	6ETY	6ETY
Glu424Met inactive mutant; complex with a inhibitor jhu3372	1.61 Å	6EZ9	6EZ9	6EZ9	6EZ9	6EZ9	6EZ9
complex with a inhibitor jhu2379	1.63 Å	6F5L	6F5L	6F5L	6F5L	6F5L	6F5L
Glu424Met inactive mutant; complex with a inhibitor jhu 2249	1.52 Å	6FE5	6FE5	6FE5	6FE5	6FE5	6FE5
complex with a inhibitor rna 1-79-1	1.81 Å	6H7Y	6H7Y	6H7Y	6H7Y	6H7Y	6H7Y
complex with a inhibitor rna 2-65-1	2.00 Å	6H7Z	6H7Z	6H7Z	6H7Z	6H7Z	6H7Z
complex with a inhibitor rna 2-19-1	2.09 Å	6HKJ	6HKJ	6HKJ	6HKJ	6HKJ	6HKJ
complex with a inhibitor rna 2-49-1	2.09 Å	6HKZ	6HKZ	6HKZ	6HKZ	6HKZ	6HKZ