4NGP - JenaLib

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Title :   CRYSTAL STRUCTURE OF GLUTAMATE CARBOXYPEPTIDASE II IN A COMPLEX WITH UREA-BASED INHIBITOR

Authors :   J. Tykvart, P. Pachl

Date :   02 Nov 13 (Deposition) - 18 Jun 14 (Release) - 18 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Hydrolase, Glutamate Carboxypeptidase Ii, Psma, Naaladase, Urea-Based Inhibitor, Caboxypeptidase, Glycoprotein, Metallopeptidase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Tykvart, J. Schimer, J. Barinkova, P. Pachl, L. Postova-Slavetinska, P. Majer, J. Konvalinka, P. Sacha
Rational Design Of Urea-Based Glutamate Carboxypeptidase Ii (Gcpii) Inhibitors As Versatile Tools For Specific Drug Targeting And Delivery
Bioorg. Med. Chem. 2014
PubMed: search | Reference-DOI: 10.1016/J.BMC.2014.05.061

Molecule 1 - GLUTAMATE CARBOXYPEPTIDASE 2
	Chains	:	A
	EC Number	:	3.4.17.21
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell Line	:	SCHNEIDER 2(S2) CELLS
	Expression System Plasmid	:	PMT/BIP
	Expression System Taxid	:	7227
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	EXTRACELLULAR DOMAIN, UNP RESIDUES 44-750
	Gene	:	FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CELL GROWTH-INHIBITING GENE 27 PROTEIN, FOLATE HYDROLASE 1, FOLYLPOLY-GAMMA-GLUTAMATE CARBOXYPEPTIDASE, FGCP, GLUTAMATE CARBOXYPEPTIDASE II, GCPII, MEMBRANE GLUTAMATE CARBOXYPEPTIDASE, MGCP, N-ACETYLATED-ALPHA-LINKED ACIDIC DIPEPTIDASE I, NAALADASE I, PROSTATE-SPECIFIC MEMBRANE ANTIGEN, PSM, PSMA, PTEROYLPOLY-GAMMA- GLUTAMATE CARBOXYPEPTIDASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 21)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	CA	1	Ligand/Ion	CALCIUM ION
3	CL	1	Ligand/Ion	CHLORIDE ION
4	J31	1	Ligand/Ion	N-{[(1S)-1-CARBOXY-5-{[2-({4,44-DIOXO-48-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]-7,10,13,16,19,22,25,28,31,34,37,40-DODECAOXA-3,43-DIAZAOCTATETRACONT-1-YL}OXY)BENZOYL]AMINO}PENTYL]CARBAMOYL}-L-GLUTAMIC ACID
5	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 34)

No.	Name	Count	Type	Full Name
1	BMA	4	Ligand/Ion	BETA-D-MANNOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	J31	2	Ligand/Ion	N-{[(1S)-1-CARBOXY-5-{[2-({4,44-DIOXO-48-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]-7,10,13,16,19,22,25,28,31,34,37,40-DODECAOXA-3,43-DIAZAOCTATETRACONT-1-YL}OXY)BENZOYL]AMINO}PENTYL]CARBAMOYL}-L-GLUTAMIC ACID
5	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	24	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:210 , ASN A:257 , ASP A:387 , GLU A:424 , GLU A:425 , GLY A:427 , LEU A:428 , GLU A:457 , ARG A:463 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , ASN A:544 , PHE A:546 , TYR A:552 , HIS A:553 , LYS A:699 , TYR A:700 , ZN A:819 , HOH A:902 , HOH A:994 , HOH A:1062 , HOH A:1084 , HOH A:1116 , HOH A:1118 , HOH A:1183 , HOH A:1193 , HOH A:1312 , HOH A:1367 , HOH A:1504	BINDING SITE FOR RESIDUE J31 A 817
02	AC2	SOFTWARE	HIS A:377 , ASP A:387 , GLU A:424 , GLU A:425 , ASP A:453 , ZN A:819 , HOH A:1367	BINDING SITE FOR RESIDUE ZN A 818
03	AC3	SOFTWARE	ASP A:387 , GLU A:425 , HIS A:553 , J31 A:817 , ZN A:818 , HOH A:1367	BINDING SITE FOR RESIDUE ZN A 819
04	AC4	SOFTWARE	ASN A:451 , ASP A:453 , ARG A:534 , ARG A:536	BINDING SITE FOR RESIDUE CL A 820
05	AC5	SOFTWARE	THR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:1136	BINDING SITE FOR RESIDUE CA A 821
06	AC6	SOFTWARE	ASN A:76 , HOH A:925 , HOH A:1000 , HOH A:1441 , HOH A:1466 , HOH A:1496	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 76 RESIDUES 804 TO 805
07	AC7	SOFTWARE	ASN A:121 , THR A:123 , HIS A:124 , THR A:349 , HOH A:1354 , HOH A:1467	BINDING SITE FOR MONO-SACCHARIDE NAG A 806 BOUND TO ASN A 121
08	AC8	SOFTWARE	TYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , HOH A:1480 , HOH A:1481	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 140 RESIDUES 802 TO 803
09	AC9	SOFTWARE	ASN A:195 , SER A:197 , HOH A:1465	BINDING SITE FOR MONO-SACCHARIDE NAG A 801 BOUND TO ASN A 195
10	BC1	SOFTWARE	TRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:939 , HOH A:1391 , HOH A:1477 , HOH A:1506 , HOH A:1507	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 459 RESIDUES 815 TO 816
11	BC2	SOFTWARE	SER A:472 , ASN A:476 , PRO A:594 , GLN A:651 , HOH A:1401 , HOH A:1469 , HOH A:1470 , HOH A:1471 , HOH A:1489	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 476 RESIDUES 812 TO 814
12	BC3	SOFTWARE	LEU A:110 , HIS A:112 , PHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , TYR A:277 , ARG A:354 , SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , HOH A:1245 , HOH A:1318 , HOH A:1320 , HOH A:1324 , HOH A:1360 , HOH A:1438	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 638 RESIDUES 807 TO 811

(no "SS Bond" information available for 4NGP)

Asymmetric Unit

No.	Residues
1	Tyr A:242	-	Pro A:243
2	Gly A:330	-	Pro A:331
3	Asp A:387	-	Pro A:388

(no "SAP(SNP)/Variant" information available for 4NGP)

(no "PROSITE Motif" information available for 4NGP)

(no "Exon" information available for 4NGP)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:695
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.......eeeee.....eeee.....................ee.......ee.eee....hhhhhhhhhhh........eeeee....hhhhhhhhhhhh...eeeee.hhhhhh....................ee........................hhhhh.......eeeehhhhhhhhhh........hhhhh.............hhhhh..eeeee...eeeeeeeeeeeeee....eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhheeeeee.........eeeeee...hhhhhhhhhh............hhhhhhhhhh...................hhhhhh.....eeeeeee.hhhhh.............hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ngp A  55 KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA 750
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654||     665       675       685       695       705       715       725       735       745     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  655|                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   657

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4NGP)

(no "CATH Domain" information available for 4NGP)

(no "Pfam Domain" information available for 4NGP)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asp A:387 - Pro A:388	[ RasMol ]
		Gly A:330 - Pro A:331	[ RasMol ]
		Tyr A:242 - Pro A:243	[ RasMol ]

Biological Unit
	Complete Structure
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	4ngp
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 21)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (22, 22)

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