Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5VXO

Crystal Structure Analysis of human CLYBL in complex with propionyl-CoA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003824	molecular_function	catalytic activity
A	0004474	molecular_function	malate synthase activity
A	0005739	cellular_component	mitochondrion
A	0016740	molecular_function	transferase activity
A	0016787	molecular_function	hydrolase activity
A	0016829	molecular_function	lyase activity
A	0046872	molecular_function	metal ion binding
A	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
A	0070207	biological_process	protein homotrimerization
A	0106064	biological_process	regulation of cobalamin metabolic process
A	0106121	biological_process	positive regulation of cobalamin metabolic process
B	0000287	molecular_function	magnesium ion binding
B	0003824	molecular_function	catalytic activity
B	0004474	molecular_function	malate synthase activity
B	0005739	cellular_component	mitochondrion
B	0016740	molecular_function	transferase activity
B	0016787	molecular_function	hydrolase activity
B	0016829	molecular_function	lyase activity
B	0046872	molecular_function	metal ion binding
B	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
B	0070207	biological_process	protein homotrimerization
B	0106064	biological_process	regulation of cobalamin metabolic process
B	0106121	biological_process	positive regulation of cobalamin metabolic process
C	0000287	molecular_function	magnesium ion binding
C	0003824	molecular_function	catalytic activity
C	0004474	molecular_function	malate synthase activity
C	0005739	cellular_component	mitochondrion
C	0016740	molecular_function	transferase activity
C	0016787	molecular_function	hydrolase activity
C	0016829	molecular_function	lyase activity
C	0046872	molecular_function	metal ion binding
C	0047777	molecular_function	(S)-citramalyl-CoA lyase activity
C	0070207	biological_process	protein homotrimerization
C	0106064	biological_process	regulation of cobalamin metabolic process
C	0106121	biological_process	positive regulation of cobalamin metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	20
Details	binding site for residue 1VU A 501

Chain	Residue
A	TYR50
A	ILE272
A	HIS273
A	PRO274
A	HOH604
A	HOH646
A	HOH647
A	HOH657
A	HOH658
B	THR313
B	MET318
A	VAL51
B	ASP320
A	LYS57
A	LYS58
A	LYS61
A	ASP76
A	GLY77
A	ARG107
A	ARG249

site_id	AC2
Number of Residues	8
Details	binding site for residue EDO A 502

Chain	Residue
A	GLY212
A	ALA213
A	THR214
B	ALA262
B	ALA263
B	LYS290
B	EDO503
B	EDO507

site_id	AC3
Number of Residues	7
Details	binding site for residue EDO A 503

Chain	Residue
A	VAL78
A	ALA79
A	ALA80
A	LYS83
A	HOH625
B	GLN305
B	MET321

site_id	AC4
Number of Residues	5
Details	binding site for residue EDO A 504

Chain	Residue
A	ILE97
A	ASP98
A	LEU99
A	LYS104
A	HOH630

site_id	AC5
Number of Residues	2
Details	binding site for residue EDO A 505

Chain	Residue
A	LYS325
C	ASP206

site_id	AC6
Number of Residues	4
Details	binding site for residue EDO A 506

Chain	Residue
A	ASP198
A	GLY237
A	GLN239
A	HOH629

site_id	AC7
Number of Residues	4
Details	binding site for residue EDO A 507

Chain	Residue
A	ASP76
A	LYS137
B	MET321
B	LYS325

site_id	AC8
Number of Residues	1
Details	binding site for residue EDO A 508

Chain	Residue
A	ASP68

site_id	AC9
Number of Residues	4
Details	binding site for residue EDO A 509

Chain	Residue
A	LYS228
A	HOH660
B	HOH601
C	EDO503

site_id	AD1
Number of Residues	5
Details	binding site for residue EDO A 510

Chain	Residue
A	GLU56
A	ARG89
A	LYS92
A	THR93
A	ILE97

site_id	AD2
Number of Residues	3
Details	binding site for residue EDO A 511

Chain	Residue
A	GLN125
A	HIS154
A	LYS156

site_id	AD3
Number of Residues	1
Details	binding site for residue EDO A 512

Chain	Residue
A	LYS82

site_id	AD4
Number of Residues	4
Details	binding site for residue PEG A 513

Chain	Residue
A	ALA334
A	THR335
A	SER336
A	ILE337

site_id	AD5
Number of Residues	1
Details	binding site for residue PEG A 514

Chain	Residue
A	VAL111

site_id	AD6
Number of Residues	6
Details	binding site for residue PEG A 515

Chain	Residue
A	GLU95
A	ASP96
A	ARG127
B	GLU121
B	GLN125
B	LYS156

site_id	AD7
Number of Residues	3
Details	binding site for residue PGE A 516

Chain	Residue
A	GLU117
A	LYS150
A	PHE153

site_id	AD8
Number of Residues	6
Details	binding site for residue PG4 A 517

Chain	Residue
A	TYR42
A	LYS234
A	GLY237
A	LEU238
A	HOH617
A	HOH699

site_id	AD9
Number of Residues	7
Details	binding site for residue PG4 A 518

Chain	Residue
A	GLU289
A	LYS290
A	TRP293
A	PHE314
A	SER317
C	THR214
C	SER215

site_id	AE1
Number of Residues	9
Details	binding site for residue PO4 A 519

Chain	Residue
C	EDO503
A	TYR224
A	LYS228
A	HOH642
A	HOH660
B	TYR224
B	LYS228
C	TYR224
C	LYS228

site_id	AE2
Number of Residues	17
Details	binding site for residue 1VU B 501

Chain	Residue
B	TYR50
B	LYS57
B	LYS58
B	LYS61
B	GLY77
B	ARG107
B	ILE272
B	HIS273
B	PRO274
B	HOH605
B	HOH607
B	HOH658
B	HOH667
C	ALA311
C	THR313
C	MET318
C	ASP320

site_id	AE3
Number of Residues	3
Details	binding site for residue EDO B 502

Chain	Residue
B	GLU139
B	THR172
B	SER210

site_id	AE4
Number of Residues	7
Details	binding site for residue EDO B 503

Chain	Residue
A	EDO502
B	LYS290
B	GLN326
B	ASN329
B	THR330
B	EDO507
B	HOH622

site_id	AE5
Number of Residues	2
Details	binding site for residue EDO B 504

Chain	Residue
B	ALA300
B	PGE514

site_id	AE6
Number of Residues	5
Details	binding site for residue EDO B 505

Chain	Residue
B	HIS304
B	THR313
B	EDO508
B	PGE514
B	HOH672

site_id	AE7
Number of Residues	3
Details	binding site for residue EDO B 506

Chain	Residue
B	TYR42
B	SER336
B	PEG513

site_id	AE8
Number of Residues	8
Details	binding site for residue EDO B 507

Chain	Residue
A	EDO502
B	GLN283
B	SER285
B	PRO286
B	LYS290
B	LEU333
B	EDO503
B	HOH647

site_id	AE9
Number of Residues	6
Details	binding site for residue EDO B 508

Chain	Residue
B	THR313
B	PHE314
B	GLN315
B	EDO505
B	PGE514
B	HOH703

site_id	AF1
Number of Residues	2
Details	binding site for residue EDO B 510

Chain	Residue
B	GLU289
B	LYS292

site_id	AF2
Number of Residues	3
Details	binding site for residue EDO B 511

Chain	Residue
B	ARG158
B	LYS159
B	HOH628

site_id	AF3
Number of Residues	1
Details	binding site for residue PEG B 512

Chain	Residue
B	TRP293

site_id	AF4
Number of Residues	6
Details	binding site for residue PEG B 513

Chain	Residue
A	SER210
B	LYS234
B	GLY237
B	LEU238
B	EDO506
B	HOH650

site_id	AF5
Number of Residues	7
Details	binding site for residue PGE B 514

Chain	Residue
B	ALA300
B	HIS304
B	THR313
B	PHE314
B	EDO504
B	EDO505
B	EDO508

site_id	AF6
Number of Residues	17
Details	binding site for residue 1VU C 501

Chain	Residue
A	ALA311
A	MET318
A	ASP320
C	TYR50
C	VAL51
C	LYS57
C	LYS58
C	LYS61
C	GLY77
C	ARG107
C	ILE272
C	HIS273
C	PRO274
C	HOH603
C	HOH615
C	HOH637
C	HOH669

site_id	AF7
Number of Residues	3
Details	binding site for residue EDO C 502

Chain	Residue
C	VAL111
C	GLU142
C	TRP146

site_id	AF8
Number of Residues	5
Details	binding site for residue EDO C 503

Chain	Residue
A	EDO509
A	PO4519
B	LYS228
B	HOH601
C	LYS228

site_id	AF9
Number of Residues	8
Details	binding site for residue EDO C 504

Chain	Residue
C	TYR42
C	ASP198
C	GLY237
C	GLN239
C	EDO506
C	PGE511
C	HOH639
C	HOH682

site_id	AG1
Number of Residues	3
Details	binding site for residue EDO C 505

Chain	Residue
C	HIS304
C	PHE312
C	THR313

site_id	AG2
Number of Residues	5
Details	binding site for residue EDO C 506

Chain	Residue
C	HIS40
C	TYR42
C	EDO504
C	PEG510
C	PGE511

site_id	AG3
Number of Residues	1
Details	binding site for residue EDO C 507

Chain	Residue
C	TRP293

site_id	AG4
Number of Residues	9
Details	binding site for residue EDO C 508

Chain	Residue
C	TYR42
C	PRO44
C	ARG45
C	ARG46
C	GLN239
C	THR267
C	PG4512
C	HOH651
C	HOH672

site_id	AG5
Number of Residues	4
Details	binding site for residue PEG C 509

Chain	Residue
C	ALA334
C	THR335
C	ILE337
C	HOH711

site_id	AG6
Number of Residues	5
Details	binding site for residue PEG C 510

Chain	Residue
C	HIS40
C	PHE196
C	EDO506
C	PGE511
C	HOH608

site_id	AG7
Number of Residues	9
Details	binding site for residue PGE C 511

Chain	Residue
C	LEU187
C	PHE196
C	LEU197
C	PHE236
C	GLY237
C	EDO504
C	EDO506
C	PEG510
C	HOH656

site_id	AG8
Number of Residues	10
Details	binding site for residue PG4 C 512

Chain	Residue
B	SER210
C	TYR42
C	LYS234
C	GLY237
C	LEU238
C	THR332
C	SER336
C	EDO508
C	HOH639
C	HOH674

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: ACT_SITE => ECO:0000269\|PubMed:29056341

Chain	Residue	Details
A	ASP320
B	ASP320
C	ASP320

site_id	SWS_FT_FI2
Number of Residues	15
Details	BINDING: BINDING => ECO:0000269\|PubMed:29056341, ECO:0007744\|PDB:5VXC, ECO:0007744\|PDB:5VXO

Chain	Residue	Details
A	TYR50
B	ILE272
C	TYR50
C	LYS57
C	LYS61
C	ARG107
C	ILE272
A	LYS57
A	LYS61
A	ARG107
A	ILE272
B	TYR50
B	LYS57
B	LYS61
B	ARG107

site_id	SWS_FT_FI3
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:29056341, ECO:0007744\|PDB:5VXC

Chain	Residue	Details
A	GLU171
A	ASP206
B	GLU171
B	ASP206
C	GLU171
C	ASP206

site_id	SWS_FT_FI4
Number of Residues	6
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q8R4N0

Chain	Residue	Details
A	LYS57
A	LYS61
B	LYS57
B	LYS61
C	LYS57
C	LYS61

site_id	SWS_FT_FI5
Number of Residues	6
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:Q8R4N0

Chain	Residue	Details
A	LYS82
A	LYS92
B	LYS82
B	LYS92
C	LYS82
C	LYS92

site_id	SWS_FT_FI6
Number of Residues	3
Details	MOD_RES: N6-succinyllysine => ECO:0000250\|UniProtKB:Q8R4N0

Chain	Residue	Details
A	LYS309
B	LYS309
C	LYS309

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