4J98 - JenaLib

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Title :   CRYSTAL STRUCTURE OF FGF RECEPTOR 2 (FGFR2) KINASE DOMAIN HARBORING THE GAIN-OF-FUNCTION K659Q MUTATION.

Authors :   Z. Huang, H. Chen, M. Mohammadi

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

Method :   X-RAY DIFFRACTION

Resolution :   2.31

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

Keywords :   Fgf Receptor, Receptor Tyrosine Kinase, Gain-Of-Function Mutation, 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 (2, 6)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ACP	-1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:625 , ARG A:649 , TYR A:657 , ARG A:664 , HOH A:1004 , HOH A:1005	BINDING SITE FOR RESIDUE SO4 A 801
2	AC2	SOFTWARE	ARG A:577 , ARG A:580 , GLY A:701	BINDING SITE FOR RESIDUE SO4 A 802
3	AC3	SOFTWARE	ARG B:625 , ARG B:649 , TYR B:657 , THR B:660 , ARG B:664 , HOH B:904 , HOH B:1003 , HOH B:1004	BINDING SITE FOR RESIDUE SO4 B 801
4	AC4	SOFTWARE	ARG B:577 , ARG B:580 , SER B:702	BINDING SITE FOR RESIDUE SO4 B 802
5	AC5	SOFTWARE	THR B:635 , ASN B:637 , VAL B:639	BINDING SITE FOR RESIDUE SO4 B 803
6	AC6	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 , ASN B:631 , LEU B:633 , ASP B:644 , HOH B:901 , HOH B:936 , HOH B:964	BINDING SITE FOR RESIDUE ACP B 804

(no "SS Bond" information available for 4J98)

Asymmetric Unit

No.	Residues
1	Tyr A:586	-	Ser A:587

(no "SAP(SNP)/Variant" information available for 4J98)

(no "PROSITE Motif" information available for 4J98)

(no "Exon" information available for 4J98)

Asymmetric Unit

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)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4j98a_ A: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..........hhh.eeeeeeeee....eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j98 A 461 AGVSEYELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGMEYSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKQTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760

Chain B from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4j98b_ B: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhh.eeeeeeeeee..eeeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j98 B 461 AGVSEYELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGMEYSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKQTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760

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 '\|'

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	d4j98a_	A:
1b	d4j98b_	B:

(no "CATH Domain" information available for 4J98)

(no "Pfam Domain" information available for 4J98)

Asymmetric Unit(hide GO term definitions)

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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:586 - Ser A:587	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	4j98
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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
4j96	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659M MUTATION
4j97	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659E MUTATION
4j99	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659T MUTATION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (133, 133)

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