BMRBj - BMREntryMaster

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BMRB: 5198

1KAT

1H, 13C, and 15N Chemical Shift Assignments for v107 in complex with vascular endothelial growth factor

Authors

Pan, B., Li, B., Russell, S.J., Tom, J.Y.K., Cochran, A.G., Fairbrother, W.J.

Assembly

peptide v107 in complex with vascular endothelial growth factor receptor-binding domain dimer

Entity

1. v107 peptide (polymer, Thiol state: all disulfide bound), 19 monomers, 2344.603 × 2 Da Detail

GGNECDIARM WEWECFERL

2. vascular endothelial growth factor (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

27955.727 Da

Max. entity weight

11633.26 Da

Entity Connection

disulfide 10 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	0:CYS16:SG	2:CYS58:SG
2	disulfide	sing	0:CYS47:SG	2:CYS92:SG
3	disulfide	sing	0:CYS51:SG	2:CYS94:SG
4	disulfide	sing	0:CYS41:SG	2:CYS50:SG
5	disulfide	sing	0:CYS16:SG	2:CYS58:SG
6	disulfide	sing	0:CYS47:SG	2:CYS92:SG
7	disulfide	sing	0:CYS51:SG	2:CYS94:SG
8	disulfide	sing	0:CYS41:SG	2:CYS50:SG
9	disulfide	sing	0:CYS5:SG	1:CYS15:SG
10	disulfide	sing	0:CYS5:SG	1:CYS15:SG

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

Torsion angle dynamics simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 20.3 %, Completeness: 18.3 %, Completeness (bb): 18.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	18.3 % (258 of 1411)	18.1 % (135 of 744)	18.6 % (101 of 544)	17.9 % (22 of 123)
Backbone	18.6 % (129 of 694)	19.1 % (45 of 236)	18.4 % (64 of 347)	18.0 % (20 of 111)
Sidechain	18.0 % (149 of 828)	17.7 % (90 of 508)	18.5 % (57 of 308)	16.7 % (2 of 12)
Aromatic	26.2 % (34 of 130)	26.2 % (17 of 65)	23.8 % (15 of 63)	100.0 % (2 of 2)
Methyl	22.7 % (20 of 88)	25.0 % (11 of 44)	20.5 % (9 of 44)

1. v107 peptide

GGNECDIARM WEWECFERL

2. vascular endothelial growth factor

HHEVVKFMDV YQRSYCHPIE TLVDIFQEYP DEIEYIFKPS CVPLMRCGGC CNDEGLECVP TEESNITMQI MRIKPHQGQH IGEMSFLQHN KCECRPKKD

Show sample condition

Sample

Temperature 308 (±0.2) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	v107 peptide	[U-98% 13C; U-98% 15N]		0.6 mM
2	vascular endothelial growth factor			0.9 mM

Protein Blocks Logo

Calculated from 24 models in PDB: 1KAT, Strand ID: V, W, X, Y Detail

Release date

2002-05-06

Citation

Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor
Pan, B., Li, B., Russell, S.J., Tom, J.Y.K., Cochran, A.G., Fairbrother, W.J.
J. Mol. Biol. (2002), 316, 769-787, PubMed 11866530 , DOI 10.1006/jmbi.2001.5370 , Abstract

Related entities 1. v107 peptide, : 1 entities Detail

Related entities 2. vascular endothelial growth factor, : 2 : 1 : 82 entities Detail

Interaction partners 2. vascular endothelial growth factor, : 19 interactors Detail

More details for 19 interactors identified by 10 citations

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr5198_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	unknown	unknown	n/a
1:47:CYS:SG	1:92:CYS:SG	unknown	unknown	n/a
1:51:CYS:SG	1:94:CYS:SG	unknown	unknown	n/a
1:41:CYS:SG	2:50:CYS:SG	unknown	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	n/a
3:5:CYS:SG	3:15:CYS:SG	unknown	unknown	n/a
4:5:CYS:SG	4:15:CYS:SG	unknown	unknown	n/a

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

None

Non-standard residues

None

Content subtype: bmr5198_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	222		100.0 (chain: 1, length: 19)
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: 19, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 122
  - ¹³C chemical shifts: 82
  - ¹⁵N chemical shifts: 18
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Rotameric state of ILE , LEU, and VAL
- 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	119	110	92.4
¹³C chemical shifts	86	82	95.3
¹⁵N chemical shifts	24	18	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	37	92.5
¹³C chemical shifts	38	35	92.1
¹⁵N chemical shifts	19	16	84.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	79	73	92.4
¹³C chemical shifts	48	47	97.9
¹⁵N chemical shifts	5	2	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	6	6	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0
¹³C chemical shifts	15	15	100.0
¹⁵N chemical shifts	2	2	100.0

Keywords vascular endothelial growth factor

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