Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4R1M

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.48 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	16
Details	BINDING SITE FOR RESIDUE AMP A 502

Chain	Residue
A	PHE237
A	GLY238
A	MSE239
A	THR240
A	ASP304
A	ARG328
A	ILE334
A	ASN339
A	EDO510
A	HOH610
A	HOH683
A	ALA214
A	GLU215
A	PRO216
A	ASN235
A	SER236

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA A 503

Chain	Residue
A	LYS128
A	GLY155
A	CYS156
A	LEU157
B	GLY87
B	HOH665

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 504

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

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 505

Chain	Residue
A	LYS45
D	TYR5
D	TRP6
D	EDO504

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

Chain	Residue
A	MSE70
A	TYR74
A	PRO75
A	LEU78
A	PRO100
A	VAL102
A	HOH695

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 507

Chain	Residue
A	GLN22
A	GLU261
A	VAL266

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 508

Chain	Residue
A	SER166
A	ARG190

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 509

Chain	Residue
A	ILE32
A	GLU293

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 510

Chain	Residue
A	MSE239
A	GLU241
A	TYR300
A	THR302
A	ARG328
A	ASN339
A	AMP502

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

Chain	Residue
A	SER135
A	ALA163
A	GLY164
A	TYR187

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 512

Chain	Residue
A	LYS28
A	THR29
A	ILE32
A	LEU290
A	ASP291
A	ARG292
A	GLU293

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 501

Chain	Residue
B	CYS251
B	HIS258
B	CYS313
B	CYS315

site_id	BC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE AMP B 502

Chain	Residue
B	ALA214
B	GLU215
B	PRO216
B	ASN235
B	SER236
B	PHE237
B	GLY238
B	MSE239
B	THR240
B	ASP304
B	ILE325
B	ARG328
B	LYS424
B	HOH627
B	HOH644
B	HOH671

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 503

Chain	Residue
A	GLY87
A	HOH638
B	LYS128
B	GLY155
B	HOH601

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 504

Chain	Residue
B	TRP6
B	HOH661

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

Chain	Residue
C	CYS251
C	HIS258
C	CYS313
C	CYS315

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NA C 502

Chain	Residue
C	ARG85
C	GLY87
D	LYS128
D	GLY155
D	CYS156
D	LEU157
C	LYS84

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA C 503

Chain	Residue
C	LYS128
C	GLY155
C	HOH653
D	LYS84
D	GLY87
D	HOH613

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL C 504

Chain	Residue
A	SER52
A	LYS61
C	LYS84
C	ARG85

site_id	CC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL C 505

Chain	Residue
C	SER166
C	ARG190

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 506

Chain	Residue
C	TYR5
C	TRP6
C	TYR122

site_id	CC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 507

Chain	Residue
A	GLU275
C	HOH643

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 508

Chain	Residue
C	THR66
C	LYS67
C	SER68
C	ARG303

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

Chain	Residue
D	CYS251
D	HIS258
D	CYS313
D	CYS315

site_id	CC8
Number of Residues	15
Details	BINDING SITE FOR RESIDUE AMP D 502

Chain	Residue
D	ALA214
D	GLU215
D	PRO216
D	ASN235
D	SER236
D	PHE237
D	GLY238
D	MSE239
D	THR240
D	ASP304
D	ARG328
D	LYS424
D	HOH624
D	HOH653
D	HOH656

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 503

Chain	Residue
D	ARG25
D	LYS28
D	LEU290
D	GLU293

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 504

Chain	Residue
A	EDO505
D	TRP6
D	GLU7

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)