BMRBj - BMREntryMaster

Found 1 Document (0.567 seconds)

BMRB: 15124

2JNR

Discovery and optimization of a natural HIV-1 entry inhibitor targeting the gp41 fusion peptide

Authors

Jiang, S., Munch, J., Standker, L., Adermann, K., Schulz, A., Pohlmann, S., Chaipan, C., Biet, T., Peters, T., Meyer, B., Wilhelm, D., Lu, H., Jing, W., Forssmann, W., Kirchhoff, F.

Assembly

Complex of VIR165 and FP1-23

Entity

1. VIR165 (polymer, Thiol state: all disulfide bound), 20 monomers, 2240.680 Da Detail

LEAIPCSIPP CFAFNKPFVF

2. FP1-23 (polymer, Thiol state: not present), 23 monomers, 2124.464 Da Detail

AVGIGALFLG FLGAAGSTMG ARS

Total weight

4365.144 Da

Max. entity weight

2240.68 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS6:SG	1:CYS11:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 73.6 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	73.6 % (178 of 242)	73.6 % (178 of 242)
Backbone	95.5 % (84 of 88)	95.5 % (84 of 88)
Sidechain	61.0 % (94 of 154)	61.0 % (94 of 154)
Aromatic	30.0 % (9 of 30)	30.0 % (9 of 30)
Methyl	84.6 % (22 of 26)	84.6 % (22 of 26)

1. VIR165

LEAIPCSIPP CFAFNKPFVF

2. FP1-23

AVGIGALFLG FLGAAGSTMG ARS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O; 3%DMSO added, Pressure 1 atm, Temperature 298 K, pH 4.7

#	Name	Isotope labeling	Concentration
1	VIR165	natural abundance	0.75 mM
2	FP1-23	natural abundance	0.75 mM
3	DMSO		3 %
4	H2O		90 %
5	D2O		10 %

Protein Blocks Logo

Calculated from 1 models in PDB: 2JNR, Strand ID: A, B Detail

Release date

2007-05-20

Citation

Discovery and optimization of a natural HIV-1 entry inhibitor targeting the gp41 fusion peptide
Munch, J., Standker, L., Adermann, K., Schulz, A., Schindler, M., Chinnadurai, R., Pohlmann, S., Chaipan, C., Biet, T., Peters, T., Meyer, B., Wilhelm, D., Lu, H., Jing, W., Jiang, S., Forssmann, W., Kirchhoff, F.
Cell (2007), 129, 263-275, PubMed 17448989 , DOI 10.1016/j.cell.2007.02.042 , Abstract

Related entities 1. VIR165, : 1 : 2 : 60 entities Detail

Related entities 2. FP1-23, : 2 : 2 : 9 : 38 entities Detail

Interaction partners 2. FP1-23, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 3 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15124_2jnr.nef
Input source #2: Coordindates	2jnr.cif
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)
A:6:CYS:SG	A:11:CYS:SG	unknown	unknown	2.034

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20
LEAIPCSIPPCFAFNKPFVF
||||||||||||||||||||
LEAIPCSIPPCFAFNKPFVF

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

-------110-------120---
AVGIGALFLGFLGAAGSTMGARS
|||||||||||||||||||||||
AVGIGALFLGFLGAAGSTMGARS
--------10--------20---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	20	0	0	100.0
B	B	23	0	0	100.0

Content subtype: combined_15124_2jnr.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	180		100.0 (chain: A, length: 20), 100.0 (chain: B, length: 23)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	31 (1)	noe	45.0 (chain: A, length: 20), 52.2 (chain: B, length: 23)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 23, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 180
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
16	LYS	HZ1	7.363
16	LYS	HZ2	7.363
16	LYS	HZ3	7.363

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	130	82	63.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	35	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	47	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	9	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	3	15.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
122	ARG	HH11	7.028
122	ARG	HH12	7.028

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	112	89	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	48	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	41	68.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	12	70.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	2	20.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 45.0%
  - Entity_assembly_ID: B, Chain length: 23, Sequence coverage: 52.2%
- Total number of restraints: 29
- Weight of restraints: 1.0 (29)
- Potential type of restraints: upper-bound-parabolic (29)
- Range of distance target values: 1.55, 5.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords Peptide complex

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Found 1 Document (0.567 seconds)

BMRB: 15124

Sample

Related entities 1. VIR165, : 1 : 2 : 60 entities Detail

Related entities 2. FP1-23, : 2 : 2 : 9 : 38 entities Detail

Interaction partners 2. FP1-23, : 1 interactors Detail

Experiments performed 3 experiments Detail

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Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail