4J95 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 4 (Jmol Viewer)

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Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FGF RECEPTOR 2 (FGFR2) KINASE DOMAIN HARBORING THE PATHOGENIC K659N MUTATION RESPONSIBLE FOR AN UNCLASSIFIED CRANIOSYNOSTOSIS SYNDROME IN SPACE GROUP C2.

Authors :   H. Chen, M. Mohammadi

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

Method :   X-RAY DIFFRACTION

Resolution :   2.38

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,B  (1x)
Biol. Unit 6: C,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	B
Biological Unit 6 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	ACP	4	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	SO4	7	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, 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 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, 5)

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

Biological Unit 6 (2, 6)

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

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:488 , GLY A:490 , ALA A:491 , VAL A:495 , ALA A:515 , LYS A:517 , VAL A:564 , GLU A:565 , ALA A:567 , ARG A:630 , ASN A:631 , LEU A:633 , ASP A:644 , HOH A:910	BINDING SITE FOR RESIDUE ACP A 801
02	AC2	SOFTWARE	ARG A:625 , ARG A:649 , TYR A:657 , THR A:660	BINDING SITE FOR RESIDUE SO4 A 802
03	AC3	SOFTWARE	THR A:635 , ASN A:637 , VAL A:639	BINDING SITE FOR RESIDUE SO4 A 803
04	AC4	SOFTWARE	LEU B:487 , GLU B:489 , GLY B:490 , ALA B:491 , VAL B:495 , ALA B:515 , VAL B:564 , GLU B:565 , ALA B:567 , ASN B:571 , ARG B:630 , ASN B:631 , LEU B:633 , ASP B:644	BINDING SITE FOR RESIDUE ACP B 801
05	AC5	SOFTWARE	ARG B:625 , ARG B:649 , TYR B:657 , THR B:660	BINDING SITE FOR RESIDUE SO4 B 802
06	AC6	SOFTWARE	GLY C:490 , ALA C:491 , VAL C:495 , ALA C:515 , LYS C:517 , GLU C:565 , ALA C:567 , ARG C:630 , LEU C:633 , ASP C:644	BINDING SITE FOR RESIDUE ACP C 801
07	AC7	SOFTWARE	ARG C:625 , ARG C:649 , TYR C:657 , ASN C:659 , THR C:660	BINDING SITE FOR RESIDUE SO4 C 802
08	AC8	SOFTWARE	THR C:635 , GLU C:636 , ASN C:637 , VAL C:639	BINDING SITE FOR RESIDUE SO4 C 803
09	AC9	SOFTWARE	ARG C:737 , LYS D:724	BINDING SITE FOR RESIDUE SO4 C 804
10	BC1	SOFTWARE	GLY D:490 , ALA D:491 , PHE D:492 , ALA D:515 , LYS D:517 , VAL D:564 , GLU D:565 , ALA D:567 , ASN D:571 , ASN D:631 , LEU D:633 , ASP D:644	BINDING SITE FOR RESIDUE ACP D 801
11	BC2	SOFTWARE	ARG D:625 , ARG D:649 , ARG D:664	BINDING SITE FOR RESIDUE SO4 D 802

(no "SS Bond" information available for 4J95)

(no "Cis Peptide Bond" information available for 4J95)

(no "SAP(SNP)/Variant" information available for 4J95)

(no "PROSITE Motif" information available for 4J95)

(no "Exon" information available for 4J95)

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:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4j95a_ 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.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j95 A 467 ELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDIYYKNTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   476       486       496       506       516       526       536       546       556       566       576    || 601       611       621       631       641       651|      665       675       685       695       705       715       725       735       745       755         
                                                                                                                                            581|                                                   651|                                                                                                            
                                                                                                                                             597                                                    656

Chain B from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4j95b_ 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.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j95 B 468 LPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKNTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   477       487       497       507       517       527       537       547       557       567       577   ||  602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762  
                                                                                                                                           581|                                                                                                                                                                       
                                                                                                                                            597

Chain C from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4j95c_ C: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eeeeeeeee....eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeee......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j95 C 468 LPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKNTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   477       487       497       507       517       527       537       547       557       567       577  ||   603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763 
                                                                                                                                          580|                                                                                                                                                                       
                                                                                                                                           597

Chain D from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains d4j95d_ D: 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....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j95 D 467 ELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDIGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   476       486       496       506       516       526       536       546       556       566       576   ||  602       612       622       632       642       663       673       683       693       703       713       723       733       743       753       763 
                                                                                                                                           580|                                                   651|                                                                                                     
                                                                                                                                            597                                                    663

Legend:		→ Mismatch	(orange background)
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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(

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Folds(

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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	d4j95a_	A:
1b	d4j95b_	B:
1c	d4j95c_	C:
1d	d4j95d_	D:

(no "CATH Domain" information available for 4J95)

(no "Pfam Domain" information available for 4J95)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
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	4j95
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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
2pvy	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659N MUTATION IN SPACE GROUP P1
4j96	FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659M MUTATION
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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (133, 133)

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