BMRBj - BMREntryMaster

Found 1 Document (1.699 seconds)

BMRB: 5186

4QAF

1H, 13C, and 15N backbone assignment of the vascular endothelial growth factor receptor-binding domain

Authors

Pan, B., Fairbrother, W.J.

Assembly

vascular endothelial growth factor receptor-binding domain dimer

Entity

1. vascular endothelial growth factor receptor-binding domain dimer (polymer, Thiol state: all disulfide bound), 99 monomers, 11633.26 × 2 Da Detail

HHEVVKFMDV YQRSYCHPIE TLVDIFQEYP DEIEYIFKPS CVPLMRCGGC CNDEGLECVP TEESNITMQI MRIKPHQGQH IGEMSFLQHN KCECRPKKD

Total weight

23266.52 Da

Max. entity weight

11633.26 Da

Entity Connection

disulfide 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	0:CYS16:SG	1:CYS58:SG
2	disulfide	sing	0:CYS47:SG	1:CYS92:SG
3	disulfide	sing	0:CYS51:SG	1:CYS94:SG
4	disulfide	sing	0:CYS41:SG	1:CYS50:SG
5	disulfide	sing	0:CYS16:SG	1:CYS58:SG
6	disulfide	sing	0:CYS47:SG	1:CYS92:SG
7	disulfide	sing	0:CYS51:SG	1:CYS94:SG
8	disulfide	sing	0:CYS41:SG	1:CYS50:SG

Source organism

Homo sapiens

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.0 %, Completeness: 50.5 %, Completeness (bb): 92.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	50.5 % (598 of 1184)	37.1 % (232 of 625)	61.1 % (280 of 458)	85.1 % (86 of 101)
Backbone	92.6 % (537 of 580)	94.9 % (186 of 196)	90.8 % (265 of 292)	93.5 % (86 of 92)
Sidechain	19.6 % (137 of 698)	11.0 % (47 of 429)	34.6 % (90 of 260)	0.0 % (0 of 9)
Aromatic	0.0 % (0 of 96)	0.0 % (0 of 48)	0.0 % (0 of 48)
Methyl	21.8 % (17 of 78)	25.6 % (10 of 39)	17.9 % (7 of 39)

1. vascular endothelial growth factor

HHEVVKFMDV YQRSYCHPIE TLVDIFQEYP DEIEYIFKPS CVPLMRCGGC CNDEGLECVP TEESNITMQI MRIKPHQGQH IGEMSFLQHN KCECRPKKD

Show sample condition

Sample #1

Temperature 318 (±0.2) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	vascular endothelial growth factor	[U-98% 13C; U-98% 15N]		1.0 mM

Sample #2

Temperature 318 (±0.2) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	vascular endothelial growth factor	[U-98% 13C; U-98% 15N]		2.0 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: -0.55 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: -0.55 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: -0.03 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.34 ppm, Outliers: 4 Detail

Release date

2002-05-06

Citation 1

1H, 13C, and 15N resonance assignment of the vascular endothelial growth factor receptor-binding domain in complex with a receptor-blocking peptide
Pan, B., Fairbrother, W.J.
J. Biomol. NMR (2002), 22, 189-190, PubMed 11883783 , Abstract

Show more 1 citaion

Citation 2

1H, 13C, and 15N backbone assignment and secondary structure of the receptor-binding domain of vascular endothelial growth factor
Fairbrother, W.J., Champe, M.A., Christinger, H.W., Keyt, B.A., Starovasnik, M.A.
Protein Sci. (1997), 6, 2250-2260, PubMed 9336848 , DOI 10.1002/pro.5560061020 , Abstract

Hide non-primary 1 citaion

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 5185 released on 2002-05-06
    Title 1H, 13C, and 15N resonance assignment of the vascular endothelial growth factor receptor-binding domain in complex with a receptor-blocking peptide
  Swiss-Prot: P15692 released on 1990-04-01
    Title VEGFA_HUMAN Entity Vascular endothelial growth factor A

Related entities 1. vascular endothelial growth factor receptor-binding domain dimer, : 1 : 32 : 12 : 97 entities Detail

Interaction partners 1. vascular endothelial growth factor receptor-binding domain dimer, : 19 interactors Detail

More details for 19 interactors identified by 10 citations

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr5186_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:16:CYS:SG	1:58:CYS:SG	oxidized, CA 55.85, CB 39.0 ppm	oxidized, CA 54.72, CB 36.3 ppm	n/a
1:47:CYS:SG	1:92:CYS:SG	oxidized, CA 57.15, CB 39.8 ppm	oxidized, CA 54.47, CB 48.5 ppm	n/a
1:51:CYS:SG	1:94:CYS:SG	unknown	oxidized, CA 56.96, CB 44.8 ppm	n/a
1:41:CYS:SG	2:50:CYS:SG	oxidized, CA 56.03, CB 39.9 ppm	unknown	n/a
2:16:CYS:SG	2:58:CYS:SG	unknown	unknown	n/a
2:47:CYS:SG	2:92:CYS:SG	unknown	unknown	n/a
2:51:CYS:SG	2:94:CYS:SG	unknown	unknown	n/a
2:41:CYS:SG	1:50:CYS:SG	unknown	unknown, CA 53.17 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr5186_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	529		94.9 (chain: 1, length: 99)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 99, Sequence coverage: 94.9%
- Total number of assignments
  - ¹H chemical shifts: 184
  - ¹³C chemical shifts: 260
  - ¹⁵N chemical shifts: 85
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	625	184	29.4
¹³C chemical shifts	458	260	56.8
¹⁵N chemical shifts	105	85	81.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	196	184	93.9
¹³C chemical shifts	198	187	94.4
¹⁵N chemical shifts	92	85	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	429	0	0.0
¹³C chemical shifts	260	73	28.1
¹⁵N chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	0	0.0
¹³C chemical shifts	44	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	0	0.0
¹³C chemical shifts	48	0	0.0

Keywords vascular endothelial growth factor

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Found 1 Document (1.699 seconds)

BMRB: 5186

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

Related entities 1. vascular endothelial growth factor receptor-binding domain dimer, : 1 : 32 : 12 : 97 entities Detail

Interaction partners 1. vascular endothelial growth factor receptor-binding domain dimer, : 19 interactors Detail

Chemical shift validation 3 contents Detail