BMRB Entry 16933

Name: Ligand Induced Changes in FKBP12 ps-ns Dynamics: FKBP12 in complex with rapamycin and the FRB domain from mTOR
Published: 2010-11-18

Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16933

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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:

Ligand Induced Changes in FKBP12 ps-ns Dynamics: FKBP12 in complex with rapamycin and the FRB domain from mTOR

Deposition date:

2010-05-14

Original release date:

2010-11-18

Authors:

Sapienza, Paul; Lee, Andrew

Citation:

Citation: Sapienza, Paul; Mauldin, Randall; Lee, Andrew. "Multi-Timescale Dynamics Study of FKBP12 Along the Rapamycin-mTOR Binding Coordinate." J. Mol. Biol. 405, 378-394 (2011).
PubMed: 21073880

Assembly members:

Assembly members:
FKBP12, polymer, 107 residues, 11819.5 Da.
FRB, polymer, 102 residues, 12227.9 Da.
RAP, non-polymer, 914.172 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: pGEX

Entity Sequences (FASTA):

Entity Sequences (FASTA):
FKBP12: GVQVETISPGDGRTFPKRGQ TCVVHYTGMLEDGKKFDSSR DRNKPFKFMLGKQEVIRGWE EGVAQMSVGQRAKLTISPDY AYGATGHPGIIPPHATLVFD VELLKLE
FRB: GSELIRVAILWHEMWHEGLE EASRLYFGERNVKGMFEVLE PLHAMMERGPQTLKETSFNQ AYGRDLMEAQEWCRKYMKSG NVKDLTQAWDLYYHVFRRIS KQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
order_parameters
- Backbone_NH_Order_Parameters

Data type	Count
13C chemical shifts	185
15N chemical shifts	94
1H chemical shifts	94
order parameters	88

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	FKBP12	1
2	rapamycin	3
3	FRB	2

Entities:

Entity 1, FKBP12 107 residues - 11819.5 Da.

1

GLY

VAL

GLN

VAL

GLU

THR

ILE

SER

PRO

GLY

2

ASP

GLY

ARG

THR

PHE

PRO

LYS

ARG

GLY

GLN

3

THR

CYS

VAL

HIS

TYR

THR

GLY

MET

LEU

4

GLU

ASP

GLY

LYS

PHE

ASP

SER

ARG

5

ASP

ARG

ASN

LYS

PRO

PHE

LYS

PHE

MET

LEU

6

GLY

LYS

GLN

GLU

VAL

ILE

ARG

GLY

TRP

GLU

7

GLU

GLY

VAL

ALA

GLN

MET

SER

VAL

GLY

GLN

8

ARG

ALA

LYS

LEU

THR

ILE

SER

PRO

ASP

TYR

9

ALA

TYR

GLY

ALA

THR

GLY

HIS

PRO

GLY

ILE

10

ILE

PRO

HIS

ALA

THR

LEU

VAL

PHE

ASP

11

VAL

GLU

LEU

LYS

LEU

GLU

Entity 3, rapamycin - C51 H79 N O13 - 914.172 Da.

1

RAP

Entity 2, FRB 102 residues - 12227.9 Da.

1

GLY

SER

GLU

LEU

ILE

ARG

VAL

ALA

ILE

LEU

2

TRP

HIS

GLU

MET

TRP

HIS

GLU

GLY

LEU

GLU

3

GLU

ALA

SER

ARG

LEU

TYR

PHE

GLY

GLU

ARG

4

ASN

VAL

LYS

GLY

MET

PHE

GLU

VAL

LEU

GLU

5

PRO

LEU

HIS

ALA

MET

GLU

ARG

GLY

PRO

6

GLN

THR

LEU

LYS

GLU

THR

SER

PHE

ASN

GLN

7

ALA

TYR

GLY

ARG

ASP

LEU

MET

GLU

ALA

GLN

8

GLU

TRP

CYS

ARG

LYS

TYR

MET

LYS

SER

GLY

9

ASN

VAL

LYS

ASP

LEU

THR

GLN

ALA

TRP

ASP

10

LEU

TYR

HIS

VAL

PHE

ARG

ILE

SER

11

LYS

GLN

Samples:

sample_1: FKBP12, [U-98% 15N], 1.5 mM; potassium phosphate 25 mM; sodium azide 0.02%; FRB 1.5 mM; rapamycin 1.5 mM; H2O 90%; D2O 10%

sample_2: FKBP12, [U-99% 13C; U-98% 15N], 1.5 mM; potassium phosphate 25 mM; sodium azide 0.02%; FRB 1.5 mM; rapamycin 1.5 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 298.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
HNCACB	sample_2	isotropic	sample_conditions_1
15N T1	sample_1	isotropic	sample_conditions_1
15N T2	sample_1	isotropic	sample_conditions_1
{1H}-15N NOE	sample_1	isotropic	sample_conditions_1

Software:

VNMR, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - data analysis

relxn2.2 - data analysis

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz
Varian INOVA 700 MHz

Related Database Links:

BMRB	11471 16925 16931 19240 19241 11471 6760
PDB	1A7X 1B6C 1BKF 1BL4 1D6O 1D7H 1D7I 1D7J 1EYM 1F40 1FAP 1FKB 1FKD 1FKF 1FKG 1FKH 1FKI 1FKJ 1FKK 1FKL 1FKR 1FKS 1FKT 1J4H 1J4I 1J4R 1NSG 1QPF 1QPL 1TCO 2DG3 2DG4 2DG9 2FAP 2FKE 2PPN 2PPO 2PPP 2RSE 3FAP 3H9R 3MDY 4DH0 4FAP 4IPX 4N19 1AUE 1FAP 1NSG 2FAP 2GAQ 2NPU 2RSE 3FAP 4DRH 4DRI 4DRJ 4FAP 4JSN 4JSP 4JSV 4JSX 4JT5 4JT6
DBJ	BAB22351 BAB27125 BAB31680 BAE32804 BAE40271 BAE06077 BAF44666 BAG10549 BAG54371
EMBL	CAA36462 CAA39272 CAA42762 CAG28541 CAG46965 CAC15570 CAC42395 CAG01719 CDQ74047
GB	AAA19163 AAA31252 AAA35844 AAA58472 AAA58476 AAA20091 AAA58486 AAA65929 AAB32957 AAC39933
PRF	1613455A 2014422A
REF	NP_000792 NP_001030533 NP_001033089 NP_001164597 NP_001239119 NP_001070679 NP_001138927 NP_001272677 NP_004949 NP_063971
SP	P18203 P26883 P62942 P62943 Q62658 P42345 P42346 Q9JLN9
TPG	DAA23300 DAA21300
AlphaFold	P18203 P26883 P62942 P62943 Q62658 P42345 P42346 Q9JLN9

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks