Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4R1L

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution

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	21
Details	BINDING SITE FOR RESIDUE ADP A 502

Chain	Residue
A	GLY238
A	MSE239
A	THR240
A	ASP304
A	ARG328
A	GLY337
A	ASN339
A	K505
A	PGE508
A	HOH613
A	HOH622
A	HOH630
A	HOH649
A	HOH656
A	HOH706
A	HOH713
A	ALA214
A	GLU215
A	PRO216
A	ASN235
A	SER236

site_id	AC3
Number of Residues	18
Details	BINDING SITE FOR RESIDUE AMP A 503

Chain	Residue
A	ALA214
A	GLU215
A	PRO216
A	ASN235
A	SER236
A	PHE237
A	GLY238
A	MSE239
A	THR240
A	ASP304
A	ARG328
A	ASN339
A	K505
A	PGE508
A	HOH613
A	HOH622
A	HOH649
A	HOH656

site_id	AC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE COA A 504

Chain	Residue
A	SER135
A	ALA163
A	GLY164
A	ASN165
A	SER166
A	ILE184
A	TYR187
A	ARG190
A	LYS336
A	THR407
A	HOH671
A	HOH733

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K A 505

Chain	Residue
A	ALA214
A	GLY337
A	ASN339
A	ADP502
A	AMP503

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE K A 506

Chain	Residue
A	MSE83
A	LYS84
A	GLY87
A	HOH768
B	LYS128
B	GLY155
B	LEU157

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K A 507

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

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PGE A 508

Chain	Residue
A	SER136
A	ALA214
A	GLY238
A	GLY337
A	ADP502
A	AMP503
A	HOH772

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 509

Chain	Residue
A	ASN165
A	SER166
A	TYR187
A	ARG190

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 510

Chain	Residue
A	GLY47
A	SER52
A	LYS61
A	HOH679
C	LYS84
C	ARG85

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 511

Chain	Residue
A	ARG393
A	ARG394
D	ARG393
D	ARG394

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 512

Chain	Residue
A	ASN31
A	ALA34
A	ILE48
A	THR49

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 513

Chain	Residue
D	TYR5
D	TRP6
D	EDO507
A	LYS45

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 514

Chain	Residue
A	MSE70
A	TYR74
A	PRO75
A	VAL102
A	MSE295

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 515

Chain	Residue
A	GLN22
A	GLU261
A	VAL266

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 501

Chain	Residue
B	CYS251
B	HIS258
B	CYS313
B	CYS315

site_id	BC8
Number of Residues	18
Details	BINDING SITE FOR RESIDUE ADP B 502

Chain	Residue
B	SER93
B	ALA214
B	PRO216
B	ASN235
B	SER236
B	PHE237
B	GLY238
B	MSE239
B	THR240
B	ASP304
B	ILE325
B	ARG328
B	LYS424
B	EDO505
B	HOH606
B	HOH645
B	HOH719
B	HOH720

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 503

Chain	Residue
B	ASN165
B	SER166
B	TYR187
B	ARG190

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 504

Chain	Residue
B	ASN46
B	ARG60
B	LYS61

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 505

Chain	Residue
B	GLY143
B	HIS182
B	ALA214
B	ADP502
B	HOH653
B	HOH720

site_id	CC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO B 506

Chain	Residue
B	TRP6

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 501

Chain	Residue
C	CYS251
C	HIS258
C	CYS313
C	CYS315

site_id	CC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE AMP C 502

Chain	Residue
C	ALA214
C	GLU215
C	PRO216
C	ASN235
C	SER236
C	GLY238
C	MSE239
C	THR240
C	ASP304
C	ARG328
C	ILE334
C	ASN339
C	K504
C	HOH627
C	HOH635
C	HOH681

site_id	CC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE COA C 503

Chain	Residue
A	HOH760
C	SER135
C	GLY164
C	ASN165
C	SER166
C	ILE184
C	TYR187
C	ARG190
C	LYS336
C	THR407
C	HOH628

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE K C 504

Chain	Residue
C	ALA214
C	GLY337
C	ASN339
C	AMP502

site_id	CC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE K C 505

Chain	Residue
C	MSE83
C	LYS84
C	GLY87
C	HOH612
D	LYS128
D	GLY155
D	LEU157

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 506

Chain	Residue
C	SER166
C	TYR187
C	ARG190

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 507

Chain	Residue
B	ARG393
C	ARG393
C	ARG394
C	HOH694

site_id	DC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 508

Chain	Residue
C	TYR5
C	TYR122

site_id	DC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 509

Chain	Residue
A	GLU275
C	GLU293

site_id	DC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 510

Chain	Residue
C	THR66
C	LYS67
C	SER68
C	ARG303
C	ASP330
C	HOH647

site_id	DC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 501

Chain	Residue
D	CYS251
D	HIS258
D	CYS313
D	CYS315

site_id	DC6
Number of Residues	17
Details	BINDING SITE FOR RESIDUE ADP D 502

Chain	Residue
D	ALA214
D	PRO216
D	ASN235
D	SER236
D	PHE237
D	GLY238
D	MSE239
D	THR240
D	ASP304
D	ILE325
D	ARG328
D	LYS424
D	PEG504
D	HOH637
D	HOH731
D	HOH733
D	HOH739

site_id	DC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE K D 503

Chain	Residue
C	LYS128
C	GLY155
C	LEU157
D	MSE83
D	LYS84
D	GLY87
D	HOH736

site_id	DC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PEG D 504

Chain	Residue
D	SER136
D	PHE141
D	HIS182
D	ILE184
D	ALA214
D	ADP502
D	HOH617
D	HOH737

site_id	DC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 D 505

Chain	Residue
D	ASN165
D	SER166
D	TYR187
D	ARG190
D	HOH634

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 506

Chain	Residue
D	ARG60
D	LYS61
D	ARG299

site_id	EC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 507

Chain	Residue
A	EDO513
D	TRP6
D	GLU7
D	ASN115

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)