5HML - JenaLib

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Title :   CRYSTAL STRUCTURE OF T5 D15 PROTEIN CO-CRYSTALLIZED WITH METAL IONS

Authors :   C. S. Flemming, M. Feng, S. E. Sedelnikova, J. Zhang, J. B. Rafferty, J. R P. J. Artymiuk

Date :   16 Jan 16 (Deposition) - 01 Jun 16 (Release) - 20 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.48

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

Keywords :   Metal Ion Complex, Flap Endonuclease, Alternative Conformations, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. A. Almalki, C. S. Flemming, J. Zhang, M. Feng, S. E. Sedelnikova, T. Ceska, J. B. Rafferty, J. R. Sayers, P. J. Artymiuk
Direct Observation Of Dna Threading In Flap Endonuclease Complexes.
Nat. Struct. Mol. Biol. V. 23 640 2016
PubMed-ID: 27273516 | Reference-DOI: 10.1038/NSMB.3241

Molecule 1 - EXODEOXYRIBONUCLEASE
	Chains	:	A, B
	EC Number	:	3.1.11.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJONEX4
	Expression System Strain	:	M72
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 20-291
	Gene	:	D15
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA PHAGE T5
	Organism Taxid	:	10726
	Other Details	:	STRUCTURE DERIVED FROM RECOMBINANT PROTEIN CORRESPONDING TO RESIDUES 20 - 291 (KNOWN AS DELTA19 AND HAD A D153K MUTATION COMPARED TO WT.
	Synonym	:	5'-EXONUCLEASE,T5FEN, T5 FLAP ENDONUCLEASE

		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, 20)

No.	Name	Count	Type	Full Name
1	B3P	1	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CL	12	Ligand/Ion	CHLORIDE ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	IOD	2	Ligand/Ion	IODIDE ION
5	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	B3P	-1	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	IOD	-1	Ligand/Ion	IODIDE ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	B3P	1	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	IOD	2	Ligand/Ion	IODIDE ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:155 , ASP A:204 , HOH A:403 , HOH A:484 , HOH A:529 , HOH A:552	binding site for residue MG A 301
02	AC2	SOFTWARE	GLU A:210	binding site for residue CL A 302
03	AC3	SOFTWARE	GLY A:213 , ARG A:216	binding site for residue CL A 303
04	AC4	SOFTWARE	ARG A:93	binding site for residue CL A 304
05	AC5	SOFTWARE	ARG A:33 , ASN A:38 , SER A:46 , THR A:50	binding site for residue EDO A 305
06	AC6	SOFTWARE	ARG A:216 , LYS A:241 , TYR A:242	binding site for residue EDO A 306
07	AC7	SOFTWARE	TYR A:90 , ALA A:91 , GLN A:92 , ARG A:93 , GLU A:95 , HOH A:518 , GLU B:182 , HIS B:183 , ASN B:185 , ALA B:214 , HOH B:562 , HOH B:576	binding site for residue B3P B 301
08	AC8	SOFTWARE	ASP B:155 , ASP B:204 , HOH B:408 , HOH B:447 , HOH B:597 , HOH B:616	binding site for residue MG B 302
09	AC9	SOFTWARE	ASP B:87 , HOH B:416 , HOH B:431 , HOH B:470 , HOH B:512 , HOH B:670	binding site for residue MG B 303
10	AD1	SOFTWARE	HOH A:614 , GLY B:213 , ARG B:216 , HOH B:656	binding site for residue CL B 304
11	AD2	SOFTWARE	PHE B:169	binding site for residue CL B 305
12	AD3	SOFTWARE	LYS B:239 , HOH B:584 , HOH B:664	binding site for residue CL B 306
13	AD4	SOFTWARE	HIS B:36	binding site for residue CL B 307
14	AD5	SOFTWARE	ASN B:38	binding site for residue CL B 308
15	AD6	SOFTWARE	SER B:45 , HOH B:682	binding site for residue CL B 309
16	AD7	SOFTWARE	LYS B:40 , PHE B:104	binding site for residue CL B 310
17	AD8	SOFTWARE	HOH B:666	binding site for residue CL B 311
18	AD9	SOFTWARE	SER B:151 , THR B:152 , PHE B:167 , SER B:168 , PHE B:169 , HOH B:493	binding site for residue CL B 312
19	AE1	SOFTWARE	ARG A:222 , LYS B:71 , HOH B:564	binding site for residue IOD B 313

(no "SS Bond" information available for 5HML)

Asymmetric Unit

No.	Residues
1	Leu A:234	-	Pro A:235
2	Leu B:234	-	Pro B:235

(no "SAP(SNP)/Variant" information available for 5HML)

(no "PROSITE Motif" information available for 5HML)

(no "Exon" information available for 5HML)

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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhh..eeee..hhhhhhhh...eeee......eehhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hml A  20 RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTKGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAE 290
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289

Chain B from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhh..eeee..hhhhhhhh...eeee......eehhhhhhhhhh..hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hml B  20 RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTKGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAE 290
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289

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 '\|'

(no "SCOP Domain" information available for 5HML)

(no "CATH Domain" information available for 5HML)

(no "Pfam Domain" information available for 5HML)

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	Cis Peptide Bonds
		Leu A:234 - Pro A:235	[ RasMol ]
		Leu B:234 - Pro B:235	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (5, 20)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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