3QYO - JenaLib

Title :   SENSITIVITY OF RECEPTOR INTERNAL MOTIONS TO LIGAND BINDING AFFINITY AND KINETIC OFF-RATE

Authors :   E. J. Collins, A. L. Lee, M. J. Carroll, R. V. Mauldin, A. V. Gromova, S. F.

Date :   03 Mar 11 (Deposition) - 18 Jan 12 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

Chains :   Asym./Biol. Unit : A

Keywords :   Rossmann Fold, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Carroll, R. V. Mauldin, A. V. Gromova, S. F. Singleton, E. J. Collins, A. L. Lee
Evidence For Dynamics In Proteins As A Mechanism For Ligand Dissociation.
Nat. Chem. Biol. V. 8 246 2012
PubMed-ID: 22246400 | Reference-DOI: 10.1038/NCHEMBIO.769

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:5 , ALA A:6 , MET A:20 , ASP A:27 , LEU A:28 , PHE A:31 , ILE A:94 , TYR A:100 , THR A:113 , HOH A:190 , NDP A:1160	BINDING SITE FOR RESIDUE Q24 A 161
02	AC2	SOFTWARE	ALA A:6 , ALA A:7 , ILE A:14 , GLY A:15 , ASN A:18 , ALA A:19 , MET A:20 , TRP A:22 , GLY A:43 , ARG A:44 , HIS A:45 , THR A:46 , LEU A:62 , SER A:63 , SER A:64 , LYS A:76 , ILE A:94 , GLY A:96 , GLY A:97 , ARG A:98 , VAL A:99 , TYR A:100 , GLN A:102 , THR A:123 , ASP A:131 , Q24 A:161 , CA A:163 , HOH A:185 , HOH A:198 , HOH A:223 , HOH A:272 , HOH A:276 , HOH A:299 , HOH A:319 , HOH A:341 , HOH A:348	BINDING SITE FOR RESIDUE NDP A 1160
03	AC3	SOFTWARE	ASP A:122 , HOH A:243 , HOH A:272 , HOH A:308 , HOH A:350	BINDING SITE FOR RESIDUE CA A 160
04	AC4	SOFTWARE	ASP A:116 , HIS A:149 , ARG A:159 , HOH A:196 , HOH A:200 , HOH A:244	BINDING SITE FOR RESIDUE CA A 162
05	AC5	SOFTWARE	ASP A:11 , HOH A:299 , NDP A:1160	BINDING SITE FOR RESIDUE CA A 163
06	AC6	SOFTWARE	PRO A:130 , TRP A:133 , HOH A:298 , HOH A:355	BINDING SITE FOR RESIDUE CA A 164
07	AC7	SOFTWARE	HOH A:228 , HOH A:249 , HOH A:250 , HOH A:286	BINDING SITE FOR RESIDUE CA A 165
08	AC8	SOFTWARE	MET A:1 , ILE A:2 , LYS A:106 , GLN A:108	BINDING SITE FOR RESIDUE CA A 166
09	AC9	SOFTWARE	SER A:49	BINDING SITE FOR RESIDUE CA A 167
10	BC1	SOFTWARE	ASN A:23 , GLN A:146 , SER A:148 , HOH A:344	BINDING SITE FOR RESIDUE CA A 168

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:159
 aligned with DYR_ECOLI | P0ABQ4 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
            DYR_ECOLI     1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
               SCOP domains d3qyoa_ A: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhh.eee........hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee..........eee.hhhhhhhhh.....eeeeehhhhhhhhh..eeeeeeeee.......ee....hhh.eeeeeeeee.........eeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------R-G---------------------------------------------------------------------------------------------------------------------------K----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------Q----- SAPs(SNPs) (2)
                PROSITE (1) DHFR_2  PDB: A:1-158 UniProt: 1-158                                                                                                                           - PROSITE (1)
                PROSITE (2) ------------DHFR_1  PDB: A:13-35   ---------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyo A   1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DYR_ECOLI | P0ABQ4)

molecular function
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0004146	dihydrofolate reductase activity	Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006545	glycine biosynthetic process	The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0031427	response to methotrexate	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methotrexate stimulus. Methotrexate is 4-amino-10-methylformic acid, a folic acid analogue that is a potent competitive inhibitor of dihydrofolate reductase.
	GO:0046654	tetrahydrofolate biosynthetic process	The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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