4J97 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FGF RECEPTOR 2 (FGFR2) KINASE DOMAIN HARBORING THE PATHOGENIC GAIN-OF-FUNCTION K659E MUTATION IDENTIFIED IN ENDOMETRIAL CANCER.

Authors :   H. Chen, M. Mohammadi

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

Method :   X-RAY DIFFRACTION

Resolution :   2.55

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A (1x),C (1x)
Biol. Unit 6: B (1x),D (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, C, D
	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	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A (1x)		C (1x)
Biological Unit 6 (1x)	:		B (1x)		D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	ACP	4	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

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, 2)

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

Biological Unit 3 (2, 2)

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

Biological Unit 4 (2, 2)

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

Biological Unit 5 (2, 3)

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

Biological Unit 6 (2, 2)

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

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:487 , GLU A:489 , ALA A:515 , GLU A:565 , TYR A:566 , ALA A:567 , ASN A:571 , LEU A:633	BINDING SITE FOR RESIDUE ACP A 801
2	AC2	SOFTWARE	ARG A:625 , ARG A:649 , TYR A:657 , ARG A:664 , HOH A:928	BINDING SITE FOR RESIDUE SO4 A 802
3	AC3	SOFTWARE	ARG A:577 , ARG A:580 , GLY A:701 , SER A:702	BINDING SITE FOR RESIDUE SO4 A 803
4	AC4	SOFTWARE	LEU B:487 , GLY B:488 , GLU B:489 , VAL B:495 , ALA B:515 , VAL B:564 , GLU B:565 , TYR B:566 , ALA B:567 , GLY B:570 , ASN B:571 , ARG B:630 , ASN B:631 , LEU B:633 , HOH B:902	BINDING SITE FOR RESIDUE ACP B 801
5	AC5	SOFTWARE	ARG B:625 , LEU B:647 , ARG B:649 , TYR B:657 , ARG B:664	BINDING SITE FOR RESIDUE SO4 B 802
6	AC6	SOFTWARE	LEU C:487 , GLY C:488 , PHE C:492 , ALA C:515 , GLU C:565 , TYR C:566 , ALA C:567 , ASN C:571 , LEU C:633 , ASP C:644 , HOH C:926 , HOH C:927	BINDING SITE FOR RESIDUE ACP C 801
7	AC7	SOFTWARE	ARG C:625 , ARG C:649 , TYR C:657 , ARG C:664	BINDING SITE FOR RESIDUE SO4 C 802
8	AC8	SOFTWARE	LEU D:487 , GLY D:488 , GLN D:494 , ALA D:515 , GLU D:565 , ALA D:567 , ASN D:571 , LEU D:633 , ASP D:644	BINDING SITE FOR RESIDUE ACP D 801
9	AC9	SOFTWARE	ARG D:625 , ARG D:649 , TYR D:657 , ARG D:664	BINDING SITE FOR RESIDUE SO4 D 802

(no "SS Bond" information available for 4J97)

Asymmetric Unit

No.	Residues
1	Pro B:582	-	Gly B:583
2	Arg D:592	-	Val D:593

(no "SAP(SNP)/Variant" information available for 4J97)

(no "PROSITE Motif" information available for 4J97)

(no "Exon" information available for 4J97)

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:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4j97a_ A: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhh.eeeeeeee..eeeeeeee.......eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee...eeee......ee......ee.......hhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j97 A 468 LPEDPKWEFPRDKLTLGKPLGEGQVVMAEAVGIDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKETTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   477       487 ||    500   ||  512       522       532       542       552       562       572       582||     602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762  
                                               489|        504|                                                                         583|                                                                                                                                                                          
                                                493         507                                                                          594

Chain B from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4j97b_ B: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eeeeeeee..eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh.......hhhhh.hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh..........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j97 B 468 LPEDPKWEFPRDKLTLGKPLGEGQVVMAEAVGIDEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKETTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   477       487 ||    500   ||  515       525       535       545       555       565       575       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761   
                                               489|        504|                                                                      583|                                                                                                                                                                              
                                                493         510                                                                       590

Chain C from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4j97c_ C: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh.eeeeeeee.eeeeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j97 C 467 ELPEDPKWEFPRDKLTLGKPLGFGQVVMAEAVGIDEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKETTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   476       486 ||    499    || 514       524       534       544       554       564       574       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761   
                                               488|         504|                                                                     582|                                                                                                                                                                              
                                                492          510                                                                      590

Chain D from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4j97d_ D: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeee...eeeeeee.........eeeeeee......hhhhhhhhhhhhhhhhhhh.......eeeee......eeee......hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee...eeee......ee......ee.......hhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh............hhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j97 D 466 YELPEDPKWEFPRDKLTLGKPLGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKETTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   475       485  ||   500       510       520       530       540       550       560       570       580 ||    599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759     
                                                488|                                                                                     582|                                                                                                                                                                            
                                                 494                                                                                      592

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	d4j97a_	A:
1b	d4j97b_	B:
1c	d4j97c_	C:
1d	d4j97d_	D:

(no "CATH Domain" information available for 4J97)

(no "Pfam Domain" information available for 4J97)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Arg D:592 - Val D:593	[ RasMol ]
		Pro B:582 - Gly B:583	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
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		Biological Unit 6	[ Jena3D ]

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	4j97
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	FGFR2_HUMAN \| P21802
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	2.7.10.1
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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
4j98	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659Q MUTATION
4j99	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659T MUTATION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (133, 133)

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