4E8Y - JenaLib

Title :   CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA HLDA IN COMPLEX WITH AN ATP-COMPETITIVE INHIBITOR

Authors :   T. -W. Lee, T. B. Verhey, M. S. Junop

Date :   20 Mar 12 (Deposition) - 26 Dec 12 (Release) - 28 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Lps-Heptose Biosynthesis, Beta-Clasp Dimerization Region, Pfkb Carbohydrate Kinase, Phosphorylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. W. Lee, T. B. Verhey, P. A. Antiperovitch, D. Atamanyuk, N. Desroy, C. Oliveira, A. Denis, V. Gerusz, E. Drocourt, S. A. Loutet, M. A. Hamad C. Stanetty, S. N. Andres, S. Sugiman-Marangos, P. Kosma, M. A. Valvano, F. Moreau, M. S. Junop
Structural-Functional Studies Of Burkholderia Cenocepacia D-Glycero-Beta-D-Manno-Heptose 7-Phosphate Kinase (Hlda) An Characterization Of Inhibitors With Antibiotic Adjuvant And Antivirulence Properties.
J. Med. Chem. V. 56 1405 2013
PubMed-ID: 23256532 | Reference-DOI: 10.1021/JM301483H

Compounds

Molecule 1 - D-BETA-D-HEPTOSE 7-PHOSPHATE KINASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HLDA, BCEJ2315_28810, BCAL2945
	Organism Scientific	:	BURKHOLDERIA CENOCEPACIA
	Organism Taxid	:	216591
	Strain	:	J2315 / LMG 16656

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 8)

Asymmetric Unit (5, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	IHA	2	Ligand/Ion	{[2-({[5-(2,6-DIMETHOXYPHENYL)-1,2,4-TRIAZIN-3-YL]AMINO}METHYL)-1,3-BENZOTHIAZOL-5-YL]OXY}ACETIC ACID
3	K	2	Ligand/Ion	POTASSIUM ION
4	M7B	1	Ligand/Ion	7-O-PHOSPHONO-D-GLYCERO-BETA-D-MANNO-HEPTOPYRANOSE
5	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IHA	2	Ligand/Ion	{[2-({[5-(2,6-DIMETHOXYPHENYL)-1,2,4-TRIAZIN-3-YL]AMINO}METHYL)-1,3-BENZOTHIAZOL-5-YL]OXY}ACETIC ACID
3	K	-1	Ligand/Ion	POTASSIUM ION
4	M7B	2	Ligand/Ion	7-O-PHOSPHONO-D-GLYCERO-BETA-D-MANNO-HEPTOPYRANOSE
5	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IHA	2	Ligand/Ion	{[2-({[5-(2,6-DIMETHOXYPHENYL)-1,2,4-TRIAZIN-3-YL]AMINO}METHYL)-1,3-BENZOTHIAZOL-5-YL]OXY}ACETIC ACID
3	K	-1	Ligand/Ion	POTASSIUM ION
4	M7B	-1	Ligand/Ion	7-O-PHOSPHONO-D-GLYCERO-BETA-D-MANNO-HEPTOPYRANOSE
5	PO4	2	Ligand/Ion	PHOSPHATE ION

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:202 , THR A:238 , ARG A:239 , SER A:240 , GLU A:241 , GLY A:243 , ALA A:257 , ALA A:259 , VAL A:262 , VAL A:265 , ALA A:268 , GLY A:269 , ASN A:294 , ALA A:297 , HOH A:631	BINDING SITE FOR RESIDUE IHA A 501
2	AC2	SOFTWARE	MET A:27 , ASP A:29 , GLY A:58 , GLY A:59 , LYS A:113 , ARG A:115 , ARG A:125 , TYR A:159 , LYS A:161 , ASP A:270	BINDING SITE FOR RESIDUE M7B A 502
3	AC3	SOFTWARE	ASP A:264 , SER A:266 , VAL A:300 , LYS A:303 , GLY A:305	BINDING SITE FOR RESIDUE K A 503
4	AC4	SOFTWARE	LEU A:57	BINDING SITE FOR RESIDUE CL A 504
5	AC5	SOFTWARE	ASN B:202 , THR B:238 , ARG B:239 , SER B:240 , GLU B:241 , GLY B:243 , ALA B:259 , ARG B:260 , VAL B:265 , ALA B:268 , GLY B:269 , ASN B:294 , ALA B:297	BINDING SITE FOR RESIDUE IHA B 501
6	AC6	SOFTWARE	LYS B:113 , LYS B:161 , HOH B:737	BINDING SITE FOR RESIDUE PO4 B 502
7	AC7	SOFTWARE	ASP B:264 , SER B:266 , VAL B:300 , LYS B:303 , GLY B:305	BINDING SITE FOR RESIDUE K B 503

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eeeeee.eeeeeeeeeeeeee......eeeeeeeeeeeeeehhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhh...eeeeeee......eeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhh..eeeee.....hhhhh...ee..hhhhhhhhhh...hhhhhhhhhhhhhhh....eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e8y A   7 VVPVPREQLARSRVLVVGDVMLDRYWFGNVDRISPEAPVPVVHVQRQEERLGGAANVARNAVTLGGQAGLLCVVGCDEPGERIVELLGSSGVTPHLERDPALPTTIKLRVLARQQQLLRVDFEAMPTHEVLLAGLARFDVLLPQHDVVLMSDYAKGGLTHVTTMIEKARAAGKAVLVDPKGDDWARYRGASLITPNRAELREVVGQWKSEDDLRARVANLRAELDIDALLLTRSEEGMTLFSAGGELHAPALAREVFDVSGAGDTVIATVATMLGAGVPLVDAVVLANRAAGIVVGKLGTATVDYDEL 314
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

Chain B from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.eeeeee.eeeeeeeeeeeeee......eeeeeeeeeeeeeehhhhhhhh.....eeeeeeeee.hhhhhhhhhhhhh..eeeeeeee......eeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhh..eeeee.....hhhhh...ee..hhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e8y B   9 PVPREQLARSRVLVVGDVMLDRYWFGNVDRISPEAPVPVVHVQRQEERLGGAANVARNAVTLGGQAGLLCVVGCDEPGERIVELLGSSGVTPHLERDPALPTTIKLRVLARQQQLLRVDFEAMPTHEVLLAGLARFDVLLPQHDVVLMSDYAKGGLTHVTTMIEKARAAGKAVLVDPKGDDWARYRGASLITPNRAELREVVGQWKSEDDLRARVANLRAELDIDALLLTRSEEGMTLFSAGGELHAPALAREVFDVSGAGDTVIATVATMLGAGVPLVDAVVLANRAAGIVVGKLGTATVDYDELF 315
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308

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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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Related Entries

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Related Entries Specified in the PDB File

4e84	CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA HLDA
4e8w	CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA HLDA IN COMPLEX WITH AN ATP-COMPETITIVE INHIBITOR
4e8z	CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA HLDA IN COMPLEX WITH AN ATP-COMPETITIVE INHIBITOR

Description