Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4RVO

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.41 A resolution

Replaces: 4R1WReplaces: 3S89

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0010124	biological_process	phenylacetate catabolic process
A	0016405	molecular_function	CoA-ligase activity
A	0016874	molecular_function	ligase activity
A	0046872	molecular_function	metal ion binding
A	0047475	molecular_function	phenylacetate-CoA ligase activity
B	0000166	molecular_function	nucleotide binding
B	0010124	biological_process	phenylacetate catabolic process
B	0016405	molecular_function	CoA-ligase activity
B	0016874	molecular_function	ligase activity
B	0046872	molecular_function	metal ion binding
B	0047475	molecular_function	phenylacetate-CoA ligase activity
C	0000166	molecular_function	nucleotide binding
C	0010124	biological_process	phenylacetate catabolic process
C	0016405	molecular_function	CoA-ligase activity
C	0016874	molecular_function	ligase activity
C	0046872	molecular_function	metal ion binding
C	0047475	molecular_function	phenylacetate-CoA ligase activity
D	0000166	molecular_function	nucleotide binding
D	0010124	biological_process	phenylacetate catabolic process
D	0016405	molecular_function	CoA-ligase activity
D	0016874	molecular_function	ligase activity
D	0046872	molecular_function	metal ion binding
D	0047475	molecular_function	phenylacetate-CoA ligase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 501

Chain	Residue
A	CYS251
A	HIS258
A	CYS313
A	CYS315

site_id	AC2
Number of Residues	22
Details	BINDING SITE FOR RESIDUE ADP A 502

Chain	Residue
A	PHE237
A	GLY238
A	MSE239
A	THR240
A	ASP304
A	ARG328
A	ILE334
A	GLY337
A	ASN339
A	K503
A	HOH615
A	HOH623
A	HOH630
A	HOH647
A	HOH681
A	HOH686
A	HOH719
A	ALA214
A	GLU215
A	PRO216
A	ASN235
A	SER236

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE K A 503

Chain	Residue
A	ALA214
A	GLY337
A	ASN339
A	ADP502

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE K A 504

Chain	Residue
A	LYS128
A	GLY155
A	CYS156
A	LEU157
B	MSE83
B	LYS84
B	GLY87
B	HOH656

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE K A 505

Chain	Residue
A	MSE83
A	LYS84
A	GLY87
A	HOH650
B	LYS128
B	GLY155
B	LEU157

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 507

Chain	Residue
A	GLY47
A	SER52
A	LYS61
C	LYS84
C	ARG85

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 508

Chain	Residue
A	ASN165
A	SER166
A	TYR187
A	ARG190

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 509

Chain	Residue
A	ARG393
A	ARG394
D	ARG393
D	ARG394

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PG4 A 510

Chain	Residue
A	LYS45
D	TYR5
D	LYS128
D	EDO506

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PEG A 511

Chain	Residue
A	ASP86
A	GLU293
A	HOH731

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PGE A 512

Chain	Residue
A	ARG60
A	GLU275

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 513

Chain	Residue
A	THR383
A	ASP384

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 514

Chain	Residue
A	ASN31
A	ALA34
A	PHE43
A	ILE48
A	THR49
A	GLY50

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 515

Chain	Residue
A	THR66
A	LYS67
A	SER68
A	ARG303

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 516

Chain	Residue
A	TYR149
A	HOH620
A	HOH702
A	HOH736
A	HOH740
A	HOH757

site_id	BC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO A 517

Chain	Residue
A	ALA80

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 501

Chain	Residue
B	CYS251
B	HIS258
B	CYS313
B	CYS315

site_id	BC9
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ADP B 502

Chain	Residue
B	THR240
B	ASP304
B	ARG328
B	LYS424
B	HOH643
B	HOH696
B	HOH719
B	SER94
B	ALA214
B	GLU215
B	PRO216
B	ASN235
B	SER236
B	PHE237
B	GLY238
B	MSE239

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 504

Chain	Residue
A	ARG398
B	ASN165
B	SER166
B	TYR187
B	ARG190

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 505

Chain	Residue
B	ARG393
B	ARG394
B	HOH705
C	ARG393
C	ARG394

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PEG B 506

Chain	Residue
B	ASN46
B	ARG60
B	LYS61

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 507

Chain	Residue
B	LYS128
B	ARG153
B	LEU154

site_id	CC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO B 508

Chain	Residue
B	TRP6

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 509

Chain	Residue
B	TRP6
B	ARG153

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 501

Chain	Residue
C	CYS251
C	HIS258
C	CYS313
C	CYS315

site_id	CC8
Number of Residues	18
Details	BINDING SITE FOR RESIDUE ADP C 502

Chain	Residue
C	ALA214
C	PRO216
C	ASN235
C	SER236
C	GLY238
C	THR240
C	ASP304
C	ILE325
C	ARG328
C	GLY337
C	ASN339
C	K503
C	HOH622
C	HOH628
C	HOH630
C	HOH631
C	HOH635
C	HOH666

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE K C 503

Chain	Residue
C	ALA214
C	GLY337
C	ASN339
C	ADP502

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE K C 504

Chain	Residue
C	MSE83
C	LYS84
C	GLY87
C	HOH690
D	LYS128
D	GLY155
D	LEU157

site_id	DC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 506

Chain	Residue
C	ASN165
C	SER166
C	TYR187
C	ARG190
C	HOH717
C	HOH718

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PGE C 507

Chain	Residue
C	TRP6
C	GLU7
C	ASN115
C	ARG153

site_id	DC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO C 509

Chain	Residue
C	ARG60

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 510

Chain	Residue
C	THR66
C	LYS67
C	ARG303

site_id	DC6
Number of Residues	17
Details	BINDING SITE FOR RESIDUE ADP D 501

Chain	Residue
D	SER93
D	ALA214
D	PRO216
D	ASN235
D	SER236
D	GLY238
D	MSE239
D	THR240
D	ASP304
D	ILE325
D	ARG328
D	LYS424
D	HOH635
D	HOH679
D	HOH680
D	HOH685
D	HOH708

site_id	DC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 502

Chain	Residue
D	CYS251
D	HIS258
D	CYS313
D	CYS315

site_id	DC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K D 503

Chain	Residue
C	LYS128
C	GLY155
C	LEU157
D	MSE83
D	LYS84
D	GLY87

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 505

Chain	Residue
D	ASN165
D	SER166
D	ARG190

site_id	EC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 506

Chain	Residue
A	PG4510
D	GLU7
D	ASN115
D	HOH712

site_id	EC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 507

Chain	Residue
D	TYR149
D	ARG153
D	HOH696

site_id	EC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 508

Chain	Residue
D	ARG60
D	LYS61
D	HOH715

Functional Information from PROSITE/UniProt

site_id	PS00697
Number of Residues	9
Details	DNA_LIGASE_A1 ATP-dependent DNA ligase AMP-binding site. DMKRDGVRI

Chain	Residue	Details
A	ASP82-ILE90

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)