5GG5 - JenaLib

Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS MUTT1

Authors :   S. M. Arif, A. G. Patil, U. Varshney, M. Vijayan

Date :   15 Jun 16 (Deposition) - 19 Apr 17 (Release) - 19 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.64

Chains :   Asym./Biol. Unit : A

Keywords :   8-Oxo-Guanine Nucleotides, Sanitization Of Nucleotide Pool, Nudix Enzyme, Histidine Phosphatase Domain, Binding Sites At Intermolecular Interface, Enzyme Action, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Arif, A. G. Patil, U. Varshney, M. Vijayan
Biochemical And Structural Studies Of Mycobacterium Smegmatis Mutt1, A Sanitization Enzyme With Unusual Modes O Association
Acta Crystallogr D Struct V. 73 349 2017 Biol
PubMed-ID: 28375146 | Reference-DOI: 10.1107/S2059798317002534
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 38)

Sites (38, 38)

Asymmetric Unit (38, 38)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:144 , ARG A:169 , HIS A:170 , ARG A:176 , ARG A:186 , ARG A:218 , LYS A:297 , HOH A:558 , HOH A:624	binding site for residue SO4 A 401
02	AC2	SOFTWARE	PRO A:146 , ARG A:149 , ARG A:153 , ARG A:178 , EDO A:412 , HOH A:566	binding site for residue SO4 A 402
03	AC3	SOFTWARE	ARG A:176 , ARG A:184 , ARG A:216 , GLU A:242 , GLU A:243 , GLN A:271 , HOH A:518 , HOH A:520 , HOH A:564 , HOH A:729	binding site for residue SO4 A 403
04	AC4	SOFTWARE	HIS A:88 , ASP A:121 , PHE A:122 , TRP A:133 , EDO A:418 , EDO A:419 , HOH A:525 , HOH A:532 , HOH A:565	binding site for residue SO4 A 404
05	AC5	SOFTWARE	ARG A:98 , THR A:100 , ARG A:109	binding site for residue SO4 A 405
06	AC6	SOFTWARE	ARG A:55 , EDO A:417 , EDO A:421 , EDO A:422 , HOH A:533 , HOH A:644	binding site for residue SO4 A 406
07	AC7	SOFTWARE	LYS A:67 , LYS A:108 , TYR A:245 , LYS A:273 , HOH A:533 , HOH A:656	binding site for residue SO4 A 407
08	AC8	SOFTWARE	SER A:123 , ASP A:189 , LYS A:190 , ARG A:193 , HOH A:517 , HOH A:582	binding site for residue SO4 A 408
09	AC9	SOFTWARE	GLY A:174 , ARG A:175 , EDO A:428 , HOH A:591 , HOH A:664	binding site for residue SO4 A 409
10	AD1	SOFTWARE	VAL A:156 , LYS A:157 , ARG A:158 , PRO A:159 , GLU A:258 , GLY A:261 , ARG A:262 , EDO A:413 , HOH A:514 , HOH A:568	binding site for residue SO4 A 410
11	AD2	SOFTWARE	GLY A:66 , LYS A:67 , EDO A:421 , HOH A:513 , HOH A:516	binding site for residue SO4 A 411
12	AD3	SOFTWARE	THR A:89 , SER A:177 , ARG A:178 , SO4 A:402	binding site for residue EDO A 412
13	AD4	SOFTWARE	PHE A:155 , VAL A:156 , ARG A:158 , GLU A:258 , SO4 A:410	binding site for residue EDO A 413
14	AD5	SOFTWARE	LYS A:157 , THR A:209 , LEU A:230 , GLN A:232 , EDO A:434 , HOH A:638	binding site for residue EDO A 414
15	AD6	SOFTWARE	LYS A:150 , ARG A:153 , MET A:204 , GLU A:229 , HOH A:593	binding site for residue EDO A 415
16	AD7	SOFTWARE	GLU A:84 , GLU A:85 , THR A:86 , GLY A:87 , ASP A:121 , PHE A:122 , SER A:123 , ASN A:125 , HOH A:511	binding site for residue EDO A 416
17	AD8	SOFTWARE	LYS A:65 , TYR A:101 , TYR A:145 , SO4 A:406	binding site for residue EDO A 417
18	AD9	SOFTWARE	LEU A:131 , SO4 A:404 , EDO A:419 , HOH A:535	binding site for residue EDO A 418
19	AE1	SOFTWARE	ARG A:33 , SO4 A:404 , EDO A:418	binding site for residue EDO A 419
20	AE2	SOFTWARE	ALA A:79 , ARG A:178 , TYR A:179 , ALA A:201 , HOH A:546	binding site for residue EDO A 420
21	AE3	SOFTWARE	LYS A:67 , LYS A:108 , SO4 A:406 , SO4 A:411 , EDO A:422	binding site for residue EDO A 421
22	AE4	SOFTWARE	TYR A:101 , LYS A:108 , LYS A:273 , SO4 A:406 , EDO A:421 , HOH A:682	binding site for residue EDO A 422
23	AE5	SOFTWARE	GLU A:280 , THR A:293 , EDO A:429	binding site for residue EDO A 423
24	AE6	SOFTWARE	TRP A:32 , VAL A:91 , GLY A:93 , VAL A:160 , THR A:162 , HOH A:609 , HOH A:712	binding site for residue EDO A 424
25	AE7	SOFTWARE	TYR A:145 , ARG A:169 , ARG A:176 , GLU A:242 , GLY A:272 , HOH A:551	binding site for residue EDO A 425
26	AE8	SOFTWARE	THR A:210 , LEU A:211 , TYR A:212 , GLN A:232 , LEU A:233 , ASP A:307	binding site for residue EDO A 426
27	AE9	SOFTWARE	GLY A:97 , ARG A:98 , LYS A:150 , GLN A:228 , GLU A:229 , GLU A:291	binding site for residue EDO A 427
28	AF1	SOFTWARE	HIS A:83 , ARG A:149 , ARG A:175 , ARG A:176 , SO4 A:409 , HOH A:604	binding site for residue EDO A 428
29	AF2	SOFTWARE	PRO A:56 , THR A:293 , GLY A:294 , EDO A:423 , HOH A:677	binding site for residue EDO A 429
30	AF3	SOFTWARE	GLN A:142 , GLN A:144 , HOH A:508 , HOH A:667	binding site for residue EDO A 430
31	AF4	SOFTWARE	LYS A:190 , ARG A:193 , HOH A:585	binding site for residue EDO A 431
32	AF5	SOFTWARE	LEU A:257 , GLY A:261 , GLY A:308 , HOH A:515 , HOH A:719	binding site for residue EDO A 432
33	AF6	SOFTWARE	MET A:204 , GLY A:207 , ALA A:208 , HOH A:563	binding site for residue EDO A 433
34	AF7	SOFTWARE	LYS A:157 , GLN A:232 , ASP A:307 , EDO A:414 , HOH A:547	binding site for residue EDO A 434
35	AF8	SOFTWARE	ARG A:193 , ALA A:196 , GLU A:197 , GLN A:221 , PRO A:225	binding site for residue EDO A 435
36	AF9	SOFTWARE	ARG A:184 , ASP A:215 , ARG A:216 , VAL A:217 , HIS A:220 , HOH A:504	binding site for residue PEG A 436
37	AG1	SOFTWARE	HIS A:54 , TRP A:61 , LYS A:130 , ARG A:191 , ARG A:296	binding site for residue PEG A 437
38	AG2	SOFTWARE	GLU A:74 , PRO A:75 , THR A:292 , TYR A:315 , LEU A:316 , SER A:317 , HOH A:549 , HOH A:694	binding site for residue PEG A 438

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

Asymmetric/Biological 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeee....eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeeee..eeeeeeeeeeeeeee.........eeeeehhhhhhhhh.hhhhhhhhhhhhhh....eeeeeee.........hhhhhhh...hhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh............eeeeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gg5 A  21 KHTVRAAGAVLWRDAHPATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDE 321
                                    30    ||  48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318   
                                         35|                                                                                                                                                                                                                                                                                     
                                          44

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		AD1	[ RasMol ]	+environment [ RasMol ]
		AD2	[ RasMol ]	+environment [ RasMol ]
		AD3	[ RasMol ]	+environment [ RasMol ]
		AD4	[ RasMol ]	+environment [ RasMol ]
		AD5	[ RasMol ]	+environment [ RasMol ]
		AD6	[ RasMol ]	+environment [ RasMol ]
		AD7	[ RasMol ]	+environment [ RasMol ]
		AD8	[ RasMol ]	+environment [ RasMol ]
		AD9	[ RasMol ]	+environment [ RasMol ]
		AE1	[ RasMol ]	+environment [ RasMol ]
		AE2	[ RasMol ]	+environment [ RasMol ]
		AE3	[ RasMol ]	+environment [ RasMol ]
		AE4	[ RasMol ]	+environment [ RasMol ]
		AE5	[ RasMol ]	+environment [ RasMol ]
		AE6	[ RasMol ]	+environment [ RasMol ]
		AE7	[ RasMol ]	+environment [ RasMol ]
		AE8	[ RasMol ]	+environment [ RasMol ]
		AE9	[ RasMol ]	+environment [ RasMol ]
		AF1	[ RasMol ]	+environment [ RasMol ]
		AF2	[ RasMol ]	+environment [ RasMol ]
		AF3	[ RasMol ]	+environment [ RasMol ]
		AF4	[ RasMol ]	+environment [ RasMol ]
		AF5	[ RasMol ]	+environment [ RasMol ]
		AF6	[ RasMol ]	+environment [ RasMol ]
		AF7	[ RasMol ]	+environment [ RasMol ]
		AF8	[ RasMol ]	+environment [ RasMol ]
		AF9	[ RasMol ]	+environment [ RasMol ]
		AG1	[ RasMol ]	+environment [ RasMol ]
		AG2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		His A:44 - Pro A:45	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5gg5
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	A0QUZ2_MYCS2 \| A0QUZ2
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description