4KBN - JenaLib

Title :   HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-{3-[3-(3,5-PYRIMIDINE)]-PHENYL-PROP-1-YN-1-YL}-6-ETHYL-PYRIMIDINE-2,4DIAMINE

Authors :   K. M. Lamb, A. C. Anderson

Date :   23 Apr 13 (Deposition) - 09 Oct 13 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

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

Keywords :   Oxidoreductase, 5, 6, 7, 8-Tetrahydrofolate, Nadp+, Hydride Shift, Cytosol, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Lamb, N. G-Dayanandan, D. L. Wright, A. C. Anderson
Elucidating Features That Drive The Design Of Selective Antifolates Using Crystal Structures Of Human Dihydrofolate Reductase.
Biochemistry V. 52 7318 2013
PubMed-ID: 24053334 | Reference-DOI: 10.1021/BI400852H

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 26)

Asymmetric Unit (7, 26)

No.	Name	Count	Type	Full Name
1	25U	2	Ligand/Ion	6-ETHYL-5-{3-[3-(PYRIMIDIN-5-YL)PHENYL]PROP-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE
2	CL	8	Ligand/Ion	CHLORIDE ION
3	EOH	3	Ligand/Ion	ETHANOL
4	MG	9	Ligand/Ion	MAGNESIUM ION
5	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
6	NH4	1	Ligand/Ion	AMMONIUM ION
7	SR	1	Ligand/Ion	STRONTIUM ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	25U	1	Ligand/Ion	6-ETHYL-5-{3-[3-(PYRIMIDIN-5-YL)PHENYL]PROP-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EOH	1	Ligand/Ion	ETHANOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
6	NH4	-1	Ligand/Ion	AMMONIUM ION
7	SR	-1	Ligand/Ion	STRONTIUM ION

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	25U	1	Ligand/Ion	6-ETHYL-5-{3-[3-(PYRIMIDIN-5-YL)PHENYL]PROP-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EOH	2	Ligand/Ion	ETHANOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
6	NH4	1	Ligand/Ion	AMMONIUM ION
7	SR	-1	Ligand/Ion	STRONTIUM ION

Sites (24, 24)

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:7 , VAL A:8 , ALA A:9 , GLU A:30 , PHE A:34 , THR A:56 , ILE A:60 , PRO A:61 , LEU A:67 , TYR A:121 , THR A:136 , NDP A:210 , HOH A:325	BINDING SITE FOR RESIDUE 25U A 201
02	AC2	SOFTWARE	VAL A:10 , SER A:11 , GLN A:12 , MET A:14 , ARG A:137 , HOH A:481	BINDING SITE FOR RESIDUE EOH A 202
03	AC3	SOFTWARE	MG A:209 , HOH A:461 , HOH A:464	BINDING SITE FOR RESIDUE CL A 203
04	AC4	SOFTWARE	GLU A:171 , LYS A:173 , GLY A:174	BINDING SITE FOR RESIDUE CL A 204
05	AC5	SOFTWARE	PRO A:160 , SER A:167 , HOH A:425	BINDING SITE FOR RESIDUE MG A 205
06	AC6	SOFTWARE	SER A:42 , VAL A:43 , HOH A:469 , MET B:139	BINDING SITE FOR RESIDUE CL A 206
07	AC7	SOFTWARE	GLN A:35 , ARG A:70	BINDING SITE FOR RESIDUE CL A 207
08	AC8	SOFTWARE	ASN A:29 , ARG A:32 , HOH A:318	BINDING SITE FOR RESIDUE CL A 208
09	AC9	SOFTWARE	ASP A:168 , GLN A:170 , CL A:203	BINDING SITE FOR RESIDUE MG A 209
10	BC1	SOFTWARE	VAL A:8 , ALA A:9 , ILE A:16 , GLY A:20 , ASP A:21 , GLY A:53 , LYS A:54 , LYS A:55 , THR A:56 , LEU A:75 , SER A:76 , ARG A:77 , GLU A:78 , ARG A:91 , VAL A:115 , GLY A:117 , SER A:118 , SER A:119 , VAL A:120 , TYR A:121 , GLU A:123 , THR A:146 , 25U A:201 , HOH A:307 , HOH A:322 , HOH A:327 , HOH A:350 , HOH A:403 , HOH A:440	BINDING SITE FOR RESIDUE NDP A 210
11	BC2	SOFTWARE	ASP A:168 , VAL A:169 , HOH A:450	BINDING SITE FOR RESIDUE MG A 211
12	BC3	SOFTWARE	GLU A:171 , GLY A:174 , VAL B:1 , GLY B:2 , SER B:3 , CL B:205	BINDING SITE FOR RESIDUE SR B 201
13	BC4	SOFTWARE	ILE B:7 , VAL B:8 , ALA B:9 , LEU B:22 , GLU B:30 , PHE B:31 , PHE B:34 , THR B:56 , ILE B:60 , PRO B:61 , LEU B:67 , VAL B:115 , TYR B:121 , THR B:136 , NDP B:214 , HOH B:327 , HOH B:358	BINDING SITE FOR RESIDUE 25U B 202
14	BC5	SOFTWARE	ASN A:185 , LYS B:173 , HOH B:456	BINDING SITE FOR RESIDUE EOH B 203
15	BC6	SOFTWARE	GLU B:62	BINDING SITE FOR RESIDUE EOH B 204
16	BC7	SOFTWARE	SER B:3 , ASN B:5 , SR B:201 , HOH B:308	BINDING SITE FOR RESIDUE CL B 205
17	BC8	SOFTWARE	ASP B:21 , NH4 B:211	BINDING SITE FOR RESIDUE MG B 206
18	BC9	SOFTWARE	PRO B:163	BINDING SITE FOR RESIDUE CL B 207
19	CC1	SOFTWARE	GLN B:35 , HOH B:346 , HOH B:366	BINDING SITE FOR RESIDUE CL B 208
20	CC2	SOFTWARE	GLN A:140 , ASP B:110	BINDING SITE FOR RESIDUE MG B 210
21	CC3	SOFTWARE	LEU B:22 , TRP B:24 , MG B:206	BINDING SITE FOR RESIDUE NH4 B 211
22	CC4	SOFTWARE	LYS B:18 , ASN B:19 , GLY B:20 , ASP B:145 , THR B:146 , NDP B:214 , HOH B:413	BINDING SITE FOR RESIDUE MG B 212
23	CC5	SOFTWARE	LEU B:153 , TYR B:156 , HOH B:336 , HOH B:445	BINDING SITE FOR RESIDUE MG B 213
24	CC6	SOFTWARE	VAL B:8 , ALA B:9 , ILE B:16 , GLY B:20 , ASP B:21 , GLY B:53 , LYS B:54 , LYS B:55 , THR B:56 , LEU B:75 , SER B:76 , ARG B:77 , GLU B:78 , ARG B:91 , VAL B:115 , GLY B:117 , SER B:118 , SER B:119 , VAL B:120 , TYR B:121 , GLU B:123 , THR B:146 , 25U B:202 , MG B:212 , HOH B:317 , HOH B:355 , HOH B:378 , HOH B:381 , HOH B:413	BINDING SITE FOR RESIDUE NDP B 214

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains d4kbna_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....eee.........hhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh....eeeeee............eee.hhhhhhhhh........eeeeee..hhhhhhhhhhh..eeeeeeeee.......ee.........eee..........eee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kbn A   1 VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains d4kbnb_ B: Dihydrofolate reductases, eukaryotic type                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....eee.........hhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh....eeeeee............eee.hhhhhhhhh........eeeeee..hhhhhhhhhh...eeeeeeeee.......ee.........ee...........eee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kbn B   1 VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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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, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (28, 28)

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