Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2A5H

2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0016853	molecular_function	isomerase activity
A	0019475	biological_process	L-lysine fermentation
A	0046872	molecular_function	metal ion binding
A	0050066	molecular_function	L-lysine 2,3-aminomutase activity
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
B	0003824	molecular_function	catalytic activity
B	0016853	molecular_function	isomerase activity
B	0019475	biological_process	L-lysine fermentation
B	0046872	molecular_function	metal ion binding
B	0050066	molecular_function	L-lysine 2,3-aminomutase activity
B	0051536	molecular_function	iron-sulfur cluster binding
B	0051539	molecular_function	4 iron, 4 sulfur cluster binding
C	0003824	molecular_function	catalytic activity
C	0016853	molecular_function	isomerase activity
C	0019475	biological_process	L-lysine fermentation
C	0046872	molecular_function	metal ion binding
C	0050066	molecular_function	L-lysine 2,3-aminomutase activity
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
D	0003824	molecular_function	catalytic activity
D	0016853	molecular_function	isomerase activity
D	0019475	biological_process	L-lysine fermentation
D	0046872	molecular_function	metal ion binding
D	0050066	molecular_function	L-lysine 2,3-aminomutase activity
D	0051536	molecular_function	iron-sulfur cluster binding
D	0051539	molecular_function	4 iron, 4 sulfur cluster binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 421

Chain	Residue
A	CYS268
B	CYS375
B	CYS377
B	CYS380

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 592

Chain	Residue
A	HIS111
A	TYR113
D	ARG409

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 421

Chain	Residue
A	CYS380
B	CYS268
A	CYS375
A	CYS377

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 593

Chain	Residue
B	ARG409
C	HIS111
C	ARG112
C	TYR113

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 421

Chain	Residue
C	CYS268
D	CYS375
D	CYS377
D	CYS380

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 494

Chain	Residue
A	ARG409
D	HIS111
D	ARG112
D	TYR113

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 421

Chain	Residue
C	CYS375
C	CYS377
C	CYS380
D	CYS268

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 495

Chain	Residue
B	HIS111
B	ARG112
B	TYR113
C	ARG409

site_id	AC9
Number of Residues	16
Details	BINDING SITE FOR RESIDUE SAM A 417

Chain	Residue
A	HIS131
A	THR133
A	ARG134
A	SER169
A	GLY171
A	HIS230
A	GLN258
A	VAL260
A	TYR290
A	GLN291
A	CYS292
A	ASP293
A	LEU298
A	SF4418
A	LYS420
A	HOH603

site_id	BC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE SAM B 417

Chain	Residue
B	HIS131
B	THR133
B	ARG134
B	SER169
B	GLY171
B	GLY200
B	HIS230
B	GLN258
B	VAL260
B	TYR290
B	GLN291
B	CYS292
B	ASP293
B	LEU298
B	SF4418
B	LYS420
B	HOH524

site_id	BC2
Number of Residues	16
Details	BINDING SITE FOR RESIDUE SAM C 417

Chain	Residue
C	HIS131
C	THR133
C	ARG134
C	SER169
C	GLY171
C	HIS230
C	GLN258
C	VAL260
C	TYR290
C	GLN291
C	CYS292
C	ASP293
C	LEU298
C	SF4418
C	LYS420
C	HOH627

site_id	BC3
Number of Residues	16
Details	BINDING SITE FOR RESIDUE SAM D 417

Chain	Residue
D	HIS131
D	THR133
D	ARG134
D	SER169
D	GLY171
D	HIS230
D	GLN258
D	VAL260
D	TYR290
D	GLN291
D	CYS292
D	ASP293
D	LEU298
D	SF4418
D	LYS420
D	HOH533

site_id	BC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LYS A 420

Chain	Residue
A	SER169
A	TYR290
A	ASP293
A	ASP330
A	SAM417
A	PLP419
A	HOH625
A	LEU118
A	ARG134
A	LEU167

site_id	BC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PLP A 419

Chain	Residue
A	THR110
A	TYR113
A	ARG116
A	LEU118
A	ARG198
A	TYR287
A	TYR288
A	LYS337
A	LYS420
A	HOH596
A	HOH600
A	HOH612
A	HOH724
B	SER320
B	GLY321

site_id	BC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LYS B 420

Chain	Residue
B	LEU118
B	ARG134
B	LEU167
B	SER169
B	TYR290
B	ASP293
B	ASP330
B	SAM417
B	PLP419
B	HOH597

site_id	BC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PLP B 419

Chain	Residue
A	SER320
A	GLY321
B	THR110
B	TYR113
B	ARG116
B	ARG198
B	TYR287
B	TYR288
B	LYS337
B	LYS420
B	HOH499
B	HOH503
B	HOH518
B	HOH592
B	HOH607

site_id	BC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LYS C 420

Chain	Residue
C	LEU118
C	ARG134
C	LEU167
C	SER169
C	TYR290
C	ASP293
C	ASP330
C	SAM417
C	PLP419
C	HOH617

site_id	BC9
Number of Residues	16
Details	BINDING SITE FOR RESIDUE PLP C 419

Chain	Residue
C	THR110
C	TYR113
C	ARG116
C	LEU118
C	ARG198
C	TYR287
C	TYR288
C	LYS337
C	LYS420
C	HOH597
C	HOH601
C	HOH606
C	HOH626
C	HOH769
D	SER320
D	GLY321

site_id	CC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LYS D 420

Chain	Residue
D	LEU118
D	ARG134
D	LEU167
D	SER169
D	TYR290
D	ASP293
D	ASP330
D	SAM417
D	PLP419
D	HOH640

site_id	CC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PLP D 419

Chain	Residue
C	SER320
C	GLY321
D	THR110
D	TYR113
D	ARG116
D	LEU118
D	ARG198
D	TYR287
D	TYR288
D	LYS337
D	LYS420
D	HOH498
D	HOH502
D	HOH659
D	HOH660

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 A 418

Chain	Residue
A	CYS125
A	CYS129
A	CYS132
A	GLY171
A	ARG202
A	HIS230
A	SAM417

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 B 418

Chain	Residue
B	CYS125
B	CYS129
B	CYS132
B	GLY171
B	ARG202
B	HIS230
B	SAM417

site_id	CC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 C 418

Chain	Residue
C	CYS125
C	CYS129
C	CYS132
C	GLY171
C	ARG202
C	HIS230
C	SAM417

site_id	CC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 D 418

Chain	Residue
D	CYS125
D	CYS129
D	CYS132
D	GLY171
D	ARG202
D	HIS230
D	SAM417
D	HOH608

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	20
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Modified residue: {"description":"N6-(pyridoxal phosphate)lysine"}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	10
Details	M-CSA 358

Chain	Residue	Details
A	LEU120	electrostatic stabiliser, hydrogen bond donor, steric role
A	ILE369	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
A	ILE121	electrostatic stabiliser, hydrogen bond donor, steric role
A	MSE124	electrostatic stabiliser, hydrogen bond acceptor, steric role
A	SER141	activator, metal ligand
A	MSE145	activator, metal ligand
A	GLU148	activator, metal ligand
A	ILE150	electrostatic stabiliser, hydrogen bond donor, steric role
A	PRO325	electrostatic stabiliser, hydrogen bond acceptor, steric role
A	ILE362	electrostatic stabiliser, hydrogen bond acceptor, steric role

site_id	MCSA2
Number of Residues	10
Details	M-CSA 358

Chain	Residue	Details
B	LEU120	electrostatic stabiliser, hydrogen bond donor, steric role
B	ILE369	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
B	ILE121	electrostatic stabiliser, hydrogen bond donor, steric role
B	MSE124	electrostatic stabiliser, hydrogen bond acceptor, steric role
B	SER141	activator, metal ligand
B	MSE145	activator, metal ligand
B	GLU148	activator, metal ligand
B	ILE150	electrostatic stabiliser, hydrogen bond donor, steric role
B	PRO325	electrostatic stabiliser, hydrogen bond acceptor, steric role
B	ILE362	electrostatic stabiliser, hydrogen bond acceptor, steric role

site_id	MCSA3
Number of Residues	10
Details	M-CSA 358

Chain	Residue	Details
C	LEU120	electrostatic stabiliser, hydrogen bond donor, steric role
C	ILE369	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
C	ILE121	electrostatic stabiliser, hydrogen bond donor, steric role
C	MSE124	electrostatic stabiliser, hydrogen bond acceptor, steric role
C	SER141	activator, metal ligand
C	MSE145	activator, metal ligand
C	GLU148	activator, metal ligand
C	ILE150	electrostatic stabiliser, hydrogen bond donor, steric role
C	PRO325	electrostatic stabiliser, hydrogen bond acceptor, steric role
C	ILE362	electrostatic stabiliser, hydrogen bond acceptor, steric role

site_id	MCSA4
Number of Residues	10
Details	M-CSA 358

Chain	Residue	Details
D	LEU120	electrostatic stabiliser, hydrogen bond donor, steric role
D	ILE369	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
D	ILE121	electrostatic stabiliser, hydrogen bond donor, steric role
D	MSE124	electrostatic stabiliser, hydrogen bond acceptor, steric role
D	SER141	activator, metal ligand
D	MSE145	activator, metal ligand
D	GLU148	activator, metal ligand
D	ILE150	electrostatic stabiliser, hydrogen bond donor, steric role
D	PRO325	electrostatic stabiliser, hydrogen bond acceptor, steric role
D	ILE362	electrostatic stabiliser, hydrogen bond acceptor, steric role

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