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NMR Structure - model 1

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NMR Structure - model 1 (Jmol Viewer)

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Description

Title :   NMR STRUCTURE OF NEUROKININ B FROM DYANA

Authors :   A. K. Mantha, I. R. Chandrashekar, N. Z. Baquer, S. M. Cowsik

Date :   12 May 03 (Deposition) - 10 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Protein, Structures From Dyana, Neuropeptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Mantha, I. R. Chandrashekar, N. Z. Baquer, S. M. Cowsik
Three Dimensional Structure Of Mammalian Tachykinin Peptide Neurokinin B Bound To Lipid Micelles.
J. Biomol. Struct. Dyn. V. 22 137 2004
PubMed-ID: 15317475
(for further references see the PDB file header)

Compounds

Molecule 1 - NEUROKININ B
	Chains	:	A
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS (HUMANS).
	Synonym	:	NKB, NEUROMEDIN K, ZNEUROK1
	Synthetic	:	YES

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1P9F)

Sites (0, 0)

(no "Site" information available for 1P9F)

SS Bonds (0, 0)

(no "SS Bond" information available for 1P9F)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1P9F)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069176	M	90	T	TKNK_HUMAN	Disease (HH10)	121918123	A	M	10	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TACHYKININ	PS00267	Tachykinin family signature.	TKNK_HUMAN	86-91	1	A:6-10

Exons (1, 1)

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2d	ENST00000300108	2d	ENSE00001516796	chr12:57410304-57410171	134	TKNK_HUMAN	-	0	0	-	-
1.3	ENST00000300108	3	ENSE00002155346	chr12:57409586-57409468	119	TKNK_HUMAN	1-38	38	0	-	-
1.4	ENST00000300108	4	ENSE00001420789	chr12:57407455-57407362	94	TKNK_HUMAN	39-70	32	0	-	-
1.5a	ENST00000300108	5a	ENSE00001107300	chr12:57407172-57407143	30	TKNK_HUMAN	70-80	11	0	-	-
1.6	ENST00000300108	6	ENSE00001107285	chr12:57406659-57406606	54	TKNK_HUMAN	80-98	19	1	A:1-10	10
1.8	ENST00000300108	8	ENSE00001775129	chr12:57406236-57406162	75	TKNK_HUMAN	98-121	24	0	-	-
1.9	ENST00000300108	9	ENSE00001516773	chr12:57406075-57405918	158	TKNK_HUMAN	-	0	0	-	-
1.10	ENST00000300108	10	ENSE00001516772	chr12:57404687-57404511	177	TKNK_HUMAN	-	0	0	-	-
1.11a	ENST00000300108	11a	ENSE00001516771	chr12:57404072-57403794	279	TKNK_HUMAN	-	0	0	-	-

Sequences/Alignments

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:10
 aligned with TKNK_HUMAN | Q9UHF0 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:10
                                    90
            TKNK_HUMAN   81 DMHDFFVGLM 90
               SCOP domains d1p9fa_ A: SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------T SAPs(SNPs)
                    PROSITE -----TACHY PROSITE
               Transcript 1 Exon 1.6   Transcript 1
                  1p9f A  1 DMHDFFVGLM 10
                                    10

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Peptides (792)

Fold: Peptide hormones (51)

Superfamily: Peptide hormones (51)

Family: Peptide hormones (51)

Protein domain: Neurokinin B (1)

Synthetic (1)

d1p9fa_

CATH Domains (0, 0)

(no "CATH Domain" information available for 1P9F)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1P9F)

Gene Ontology (8, 8)

NMR Structure(hide GO term definitions)

Chain A (TKNK_HUMAN | Q9UHF0)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0007565	female pregnancy	The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
	GO:0007218	neuropeptide signaling pathway	The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor.
	GO:0007217	tachykinin receptor signaling pathway	The series of molecular signals generated as a consequence of a tachykinin, i.e. a short peptide with the terminal sequence (Phe-X-Gly-Leu-Met-NH2), binding to a cell surface receptor.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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