4J96 - JenaLib

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Title :   CRYSTAL STRUCTURE OF FGF RECEPTOR 2 (FGFR2) KINASE DOMAIN HARBORING THE PATHOGENIC GAIN-OF-FUNCTION K659M MUTATION IDENTIFIED IN CERVICAL CANCER.

Authors :   H. Chen, M. Mohammadi

Date :   15 Feb 13 (Deposition) - 07 Aug 13 (Release) - 28 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Kinase Domain Fold Consisting Of N- And C-Lobes, Receptor Tyrosine Kinase, Atp Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Chen, Z. Huang, K. Dutta, S. Blais, T. A. Neubert, X. Li, D. Cowburn, N. J. Traaseth, M. Mohammadi
Cracking The Molecular Origin Of Intrinsic Tyrosine Kinase Activity Through Analysis Of Pathogenic Gain-Of-Function Mutations.
Cell Rep V. 4 376 2013
PubMed-ID: 23871672 | Reference-DOI: 10.1016/J.CELREP.2013.06.025

Molecule 1 - FIBROBLAST GROWTH FACTOR RECEPTOR 2
	Chains	:	A, B
	EC Number	:	2.7.10.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)PLYS-S
	Expression System Taxid	:	469008
	Fragment	:	HUMAN FGF RECEPTOR 2 KINASE DOMAIN (UNP RESIDUES 458-768)
	Gene	:	BEK, FGFR2, KGFR, KSAM
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FGFR-2, K-SAM, KGFR, KERATINOCYTE GROWTH FACTOR RECEPTOR

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	FLC	2	Ligand/Ion	CITRATE ANION
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACP	-1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	FLC	1	Ligand/Ion	CITRATE ANION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	FLC	1	Ligand/Ion	CITRATE ANION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	FLC	2	Ligand/Ion	CITRATE ANION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:577 , ARG A:580 , GLY A:701	BINDING SITE FOR RESIDUE SO4 A 801
2	AC2	SOFTWARE	LYS A:526 , ARG A:625 , ARG A:649 , TYR A:657 , MET A:659 , THR A:660 , GLY A:663 , ARG A:664 , LEU A:665	BINDING SITE FOR RESIDUE FLC A 802
3	AC3	SOFTWARE	ARG B:577 , ARG B:580 , GLY B:701 , SER B:702	BINDING SITE FOR RESIDUE SO4 B 801
4	AC4	SOFTWARE	THR B:635 , ASN B:637 , VAL B:639	BINDING SITE FOR RESIDUE SO4 B 802
5	AC5	SOFTWARE	LEU B:487 , GLY B:488 , GLU B:489 , GLY B:490 , ALA B:491 , ALA B:515 , VAL B:564 , GLU B:565 , TYR B:566 , ALA B:567 , ASN B:571 , LEU B:633 , ASP B:644 , MG B:805 , HOH B:988 , HOH B:989 , HOH B:990	BINDING SITE FOR RESIDUE ACP B 803
6	AC6	SOFTWARE	LYS B:526 , ARG B:625 , ARG B:649 , TYR B:657 , THR B:660 , GLY B:663 , ARG B:664	BINDING SITE FOR RESIDUE FLC B 804
7	AC7	SOFTWARE	LYS B:517 , ASP B:644 , ACP B:803	BINDING SITE FOR RESIDUE MG B 805

(no "SS Bond" information available for 4J96)

(no "Cis Peptide Bond" information available for 4J96)

(no "SAP(SNP)/Variant" information available for 4J96)

(no "PROSITE Motif" information available for 4J96)

(no "Exon" information available for 4J96)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4j96a_ A: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhh.eeeeeeeee....eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh..........hhhhh.hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j96 A 461 AGVSEYELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKMTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLTTN 766
                                   470       480       490       500       510       520       530       540       550       560       570       580 ||    594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764  
                                                                                                                                                   582|                                                                                                                                                                                   
                                                                                                                                                    587

Chain B from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4j96b_ B: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhh.eeeeeeeee....eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j96 B 462 GVSEYELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGMEYSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKMTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLTTN 766
                                   471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: Protein kinases, catalytic subunit (1977)

Protein domain: Fibroblast growth factor receptor 2 (16)

Human (Homo sapiens) [TaxId: 9606] (16)

1a	d4j96a_	A:
1b	d4j96b_	B:

(no "CATH Domain" information available for 4J96)

(no "Pfam Domain" information available for 4J96)

Asymmetric Unit(hide GO term definitions)

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		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4j96)

Biological Units
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		Biological Unit 2	[ Jena3D ]
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	4j96
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	2.7.10.1
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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2psq	UNPHOSPHORYLATED UNACTIVATED WILD TYPE FGFR2 KINASE DOMAIN
2pvf	PHOSPHORYLATED ACTIVATED FGFR2 KINASE DOMAIN
4j95	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659N MUTATION IN SPACE GROUP C2
4j97	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659E MUTATION
4j98	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659Q MUTATION
4j99	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659T MUTATION

Description

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Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (133, 133)

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