4TMX - JenaLib

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Title :   TRANSLATION INITIATION FACTOR EIF5B (517-858) MUTANT D533N FROM C. THERMOPHILUM, BOUND TO GTP AND SODIUM

Authors :   B. Kuhle, R. Ficner

Date :   02 Jun 14 (Deposition) - 24 Sep 14 (Release) - 24 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Translation Factor, Gtpase, Monovalent Cation, Translation Initiation, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Kuhle, R. Ficner
A Monovalent Cation Acts As Structural And Catalytic Cofactor In Translational Gtpases.
Embo J. V. 33 2547 2014
PubMed-ID: 25225612 | Reference-DOI: 10.15252/EMBJ.201488517

Molecule 1 - EIF5B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA2
	Expression System Vector Type	:	PLASMID
	Fragment	:	G DOMAIN AND DOMAIN II
	Mutation	:	YES
	Organism Scientific	:	CHAETOMIUM THERMOPHILUM
	Organism Taxid	:	209285

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 21)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	EDO	14	Ligand/Ion	1,2-ETHANEDIOL
3	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	ACY	-1	Ligand/Ion	ACETIC ACID
2	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
3	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (3, 9)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
3	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:532 , ASN A:533 , THR A:534 , GLY A:535 , LYS A:536 , THR A:537 , LYS A:538 , GLN A:549 , GLY A:555 , ILE A:556 , THR A:557 , GLY A:597 , ASN A:648 , LYS A:649 , ASP A:651 , ARG A:652 , SER A:716 , ALA A:717 , HIS A:718 , NA A:902 , MG A:903 , HOH A:1085 , HOH A:1086 , HOH A:1089 , HOH A:1110 , HOH A:1200 , HOH A:1272 , HOH A:1307 , HOH A:1395	binding site for residue GTP A 901
02	AC2	SOFTWARE	ASN A:533 , GLY A:555 , ILE A:556 , GTP A:901	binding site for residue NA A 902
03	AC3	SOFTWARE	THR A:537 , THR A:557 , GTP A:901 , HOH A:1085 , HOH A:1086	binding site for residue MG A 903
04	AC4	SOFTWARE	VAL A:576 , VAL A:577 , LYS A:579 , ASN A:662 , GLY A:663 , GLU A:666 , HOH A:1094 , HOH A:1365	binding site for residue EDO A 904
05	AC5	SOFTWARE	LYS A:673 , GLN A:676 , ARG A:680	binding site for residue EDO A 905
06	AC6	SOFTWARE	GLU A:678 , ASN A:681 , HOH A:1063	binding site for residue EDO A 906
07	AC7	SOFTWARE	CYS A:734 , GLN A:735 , MET A:738 , SER A:740 , MET A:743 , HOH A:1265	binding site for residue EDO A 907
08	AC8	SOFTWARE	HIS A:598 , GLU A:599 , HOH A:1090 , HOH A:1204 , LYS B:579 , ASP B:580 , GLY B:581	binding site for residue EDO A 908
09	AC9	SOFTWARE	GLN A:572 , LYS A:573	binding site for residue EDO A 909
10	AD1	SOFTWARE	HOH A:1001 , LEU B:521 , LYS B:586 , HOH B:1012 , HOH B:1038	binding site for residue EDO A 910
11	AD2	SOFTWARE	VAL B:532 , ASN B:533 , THR B:534 , GLY B:535 , LYS B:536 , THR B:537 , LYS B:538 , GLN B:549 , GLY B:555 , ILE B:556 , THR B:557 , GLY B:597 , ASN B:648 , LYS B:649 , ASP B:651 , ARG B:652 , SER B:716 , ALA B:717 , HIS B:718 , NA B:902 , MG B:903 , HOH B:1088 , HOH B:1089 , HOH B:1091 , HOH B:1179 , HOH B:1199 , HOH B:1279 , HOH B:1380	binding site for residue GTP B 901
12	AD3	SOFTWARE	ASN B:533 , GLY B:555 , ILE B:556 , GTP B:901 , HOH B:1089	binding site for residue NA B 902
13	AD4	SOFTWARE	THR B:537 , THR B:557 , GTP B:901 , HOH B:1088 , HOH B:1089	binding site for residue MG B 903
14	AD5	SOFTWARE	VAL B:532 , ASN B:533 , THR B:534 , ASP B:620 , HIS B:623 , GLU B:626 , LYS B:649 , HOH B:1162 , HOH B:1247 , HOH B:1388	binding site for residue EDO B 904
15	AD6	SOFTWARE	PRO B:642 , PHE B:643 , ARG B:708 , VAL B:710 , ARG B:737	binding site for residue EDO B 905
16	AD7	SOFTWARE	HIS A:813 , TYR B:701 , GLU B:702 , ASN B:703	binding site for residue EDO B 906
17	AD8	SOFTWARE	LEU B:748 , GLY B:772 , ILE B:773 , ARG B:775 , HOH B:1141 , HOH B:1180 , HOH B:1384	binding site for residue EDO B 907
18	AD9	SOFTWARE	ARG B:794 , SER B:826 , ALA B:827 , PRO B:828 , HOH B:1147	binding site for residue EDO B 908
19	AE1	SOFTWARE	PRO B:799 , ALA B:800 , ARG B:803 , GLY B:809 , GLN B:810 , HOH B:1184 , HOH B:1224 , HOH B:1264 , HOH B:1419	binding site for residue EDO B 909
20	AE2	SOFTWARE	ALA B:562 , THR B:563 , THR B:798 , PRO B:799 , LEU B:805 , GLN B:821 , GLY B:822 , HOH B:1113 , HOH B:1420	binding site for residue EDO B 910
21	AE3	SOFTWARE	TYR B:564 , PRO B:801 , GLN B:821 , HOH B:1113 , HOH B:1382 , HOH B:1405	binding site for residue ACY B 911

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

Asymmetric Unit

No.	Residues
1	Ala A:819	-	Ala A:820
2	Ala B:819	-	Ala B:820

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

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

(no "Exon" information available for 4TMX)

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
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Chain A from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh...eeeeee....hhhhhhhhhhh.hhhhhhhhhh....eeeeeehhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhh..eeeeeehhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee.hhh......eeeee.......hhhhhhhhhhhhhhhh.hhhhhh....eeeeeeeeee...eeeeeeeeee.eee...eeeeee..eeeeee..eeee.............ee..eee..eeeeee............eee.....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tmx A 515 HMNKDNLRSPICCILGHVNTGKTKLLDKIRQTNVQEGEAGGITQQIGATYFPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTSAHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGVTIDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPMRELRIKGQYIHHKEVKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVE 856
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854

Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee....hhhhhhhhhhh.hhhhhhhhhh....eeeeeehhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhh...eeeeeehhhhh.........hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eee.hhh......eeeee.......hhhhhhhhhhhhhhhh.hhhhhh....eeeeeeeeee...eeeeeeeeee.eee...eeee......eeee..eeee.............eee.eee..eeeeee............eee.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tmx B 514 GHMNKDNLRSPICCILGHVNTGKTKLLDKIRQTNVQEGEAGGITQQIGATYFPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTSAHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGVTIDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPMRELRIKGQYIHHKEVKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVESD 858
                                   523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853

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 '\|'

(no "SCOP Domain" information available for 4TMX)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:819 - Ala A:820	[ RasMol ]
		Ala B:819 - Ala B:820	[ RasMol ]

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	IF2P_CHATD \| G0S8G9	:	4n3g 4n3n 4ncl 4ncn 4tmt 4tmv 4tmw 4tmz 4tn1

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 21)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Gene Ontology (9, 9)

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