BMRB Entry 5981

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PDB ID: 1yho
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR5981
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

1H, 15N and 13C resonance assignments of human dihydrofolate reductase in its complex with trimethoprim and NADPH

Deposition date:

2003-10-23

Original release date:

2006-01-19

Authors:

Kovalevskaya, Nadezhda; Polshakov, Vladimir; Birdsall, Berry; Bradbury, Alan; Frenkiel, Thomas; Feeney, James

Citation:

Citation: Kovalevskaya, Nadezhda; Smurnyy, Yegor; Polshakov, Vladimir; Birdsall, Berry; Bradbury, Alan; Frenkiel, Thomas; Feeney, James. "Solution structure of human dihydrofolate reductase in its complex with trimethoprim and NADPH " J. Biomol. NMR 33, 69-72 (2005).
PubMed: 16222560

Assembly members:

Assembly members:
Dihydrofolate reductase, polymer, 186 residues, 21300 Da.
NAP, non-polymer, 743.405 Da.
TOP, non-polymer, 290.318 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: plasmid

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dihydrofolate reductase: VGSLNCIVAVSQNMGIGKNG DLPWPPLRNEFRYFQRMTTT SSVEGKQNLVIMGKKTWFSI PEKNRPLKGRINLVLSRELK EPPQGAHFLSRSLDDALKLT EQPELANKVDMVWIVGGSSV YKEAMNHPGHLKLFVTRIMQ DFESDTFFPEIDLEKYKLLP EYPGVLSDVQEEKGIKYKFE VYEKND

Data sets:

assigned_chemical_shifts

Data type	Count
1H chemical shifts	1146
13C chemical shifts	706
15N chemical shifts	204

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	dihydrofolate reductase	1
2	trimethoprim	3
3	NADPH	2

Entities:

Entity 1, dihydrofolate reductase 186 residues - 21300 Da.

1

VAL

GLY

SER

LEU

ASN

CYS

ILE

VAL

ALA

VAL

2

SER

GLN

ASN

MET

GLY

ILE

GLY

LYS

ASN

GLY

3

ASP

LEU

PRO

TRP

PRO

LEU

ARG

ASN

GLU

4

PHE

ARG

TYR

PHE

GLN

ARG

MET

THR

5

SER

VAL

GLU

GLY

LYS

GLN

ASN

LEU

VAL

6

ILE

MET

GLY

LYS

THR

TRP

PHE

SER

ILE

7

PRO

GLU

LYS

ASN

ARG

PRO

LEU

LYS

GLY

ARG

8

ILE

ASN

LEU

VAL

LEU

SER

ARG

GLU

LEU

LYS

9

GLU

PRO

GLN

GLY

ALA

HIS

PHE

LEU

SER

10

ARG

SER

LEU

ASP

ALA

LEU

LYS

LEU

THR

11

GLU

GLN

PRO

GLU

LEU

ALA

ASN

LYS

VAL

ASP

12

MET

VAL

TRP

ILE

VAL

GLY

SER

VAL

13

TYR

LYS

GLU

ALA

MET

ASN

HIS

PRO

GLY

HIS

14

LEU

LYS

LEU

PHE

VAL

THR

ARG

ILE

MET

GLN

15

ASP

PHE

GLU

SER

ASP

THR

PHE

PRO

GLU

16

ILE

ASP

LEU

GLU

LYS

TYR

LYS

LEU

PRO

17

GLU

TYR

PRO

GLY

VAL

LEU

SER

ASP

VAL

GLN

18

GLU

LYS

GLY

ILE

LYS

TYR

LYS

PHE

GLU

19

VAL

TYR

GLU

LYS

ASN

ASP

Entity 3, trimethoprim - C14 H18 N4 O3 - 290.318 Da.

1

TOP

Entity 2, NADPH - C21 H28 N7 O17 P3 - 743.405 Da.

1

NAP

Samples:

unl-DHFR-TMP-NADPH: Dihydrofolate reductase0.5 – 1.2 mM; TRIMETHOPRIM0.5 – 1.2 mM; NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE0.5 – 1.2 mM; potassium phosphate 50 mM; potassium chloride 100 mM

13C-15N-DHFR-TMP-NADPH: Dihydrofolate reductase, [U-98% 13C; U-98% 15N], 0.5 – 1.0 mM; TRIMETHOPRIM0.5 – 1.0 mM; NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE0.5 – 1.0 mM; potassium phosphate 50 mM; potassium chloride 100 mM

15N-DHFR-TMP-NADPH: Dihydrofolate reductase, [U-98% 15N], 0.75 – 1.2 mM; TRIMETHOPRIM0.75 – 1.2 mM; NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE0.75 – 1.2 mM; potassium phosphate 50 mM; potassium chloride 100 mM

condition_1: pH: 6.5; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	not available	not available	condition_1
2D NOESY	not available	not available	condition_1
2D 1H-15N HSQC	not available	not available	condition_1
2D 1H-13C HSQC	not available	not available	condition_1
3D HNCA	not available	not available	condition_1
3D HN(CO)CA	not available	not available	condition_1
3D HNHA	not available	not available	condition_1
3D HNHB	not available	not available	condition_1
3D HNCO	not available	not available	condition_1
3D HNCACB	not available	not available	condition_1
3D CBCA(CO)NH	not available	not available	condition_1
3D HBHA(CO)NH	not available	not available	condition_1
3D 1H-15N HSQC-NOESY	not available	not available	condition_1
3D 1H-13C HSQC-NOESY	not available	not available	condition_1
3D 1H-13C NOESY-HMQC	not available	not available	condition_1
3D HCCH-TOCSY	not available	not available	condition_1
2D 1H-1H 13C-FILTERED NOESY	not available	not available	condition_1
2D 1H-1H 15N-FILTERED NOESY	not available	not available	condition_1

Software:

VNMR v6.1 - spectra collecting

NMRPipe v2.1 - spectra processing

Sparky v3.06 - spectra analysis, signal assignment

NMRTABLE v2.0 - analysis of resonance assignment

NMR spectrometers:

Varian UNITY 600 MHz
Varian INOVA 600 MHz
Varian INOVA 800 MHz

BMRB	17096 19563 19564 19565 19566 19567 7195
PDB	1BOZ 1DHF 1DLR 1DLS 1DRF 1HFP 1HFQ 1HFR 1KMS 1KMV 1MVS 1MVT 1OHJ 1OHK 1PD8 1PD9 1PDB 1S3U 1S3V 1S3W 1U71 1U72 1YHO 2C2S 2C2T 2DHF 2W3A 2W3B 2W3M 3EIG 3F8Y 3F8Z 3F91 3FS6 3GHC 3GHV 3GHW 3GI2 3GYF 3L3R 3N0H 3NTZ 3NU0 3NXO 3NXR 3NXT 3NXV 3NXX 3NXY 3NZD 3OAF 3S3V 3S7A 4DDR 4G95 4KAK 4KBN 4KD7 4KEB 4KFJ 4M6J 4M6K 4M6L
DBJ	BAG35526 BAG56693 BAG59770 BAJ20267
EMBL	CAA23765 CAA25409
GB	AAA58484 AAA58485 AAH00192 AAH03584 AAH70280
PRF	0905195A 0906214A
REF	NP_000782 NP_001277283 NP_001277286 XP_001099963 XP_001110551
SP	P00374
AlphaFold	P00374