Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2YNM

Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005524	molecular_function	ATP binding
A	0015979	biological_process	photosynthesis
A	0015995	biological_process	chlorophyll biosynthetic process
A	0016491	molecular_function	oxidoreductase activity
A	0016636	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
A	0016730	molecular_function	oxidoreductase activity, acting on iron-sulfur proteins as donors
A	0019685	biological_process	photosynthesis, dark reaction
A	0036068	biological_process	light-independent chlorophyll biosynthetic process
A	0046872	molecular_function	metal ion binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
B	0005524	molecular_function	ATP binding
B	0015979	biological_process	photosynthesis
B	0015995	biological_process	chlorophyll biosynthetic process
B	0016491	molecular_function	oxidoreductase activity
B	0016636	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
B	0016730	molecular_function	oxidoreductase activity, acting on iron-sulfur proteins as donors
B	0019685	biological_process	photosynthesis, dark reaction
B	0036068	biological_process	light-independent chlorophyll biosynthetic process
B	0046872	molecular_function	metal ion binding
B	0051539	molecular_function	4 iron, 4 sulfur cluster binding
C	0005524	molecular_function	ATP binding
C	0015979	biological_process	photosynthesis
C	0015995	biological_process	chlorophyll biosynthetic process
C	0016491	molecular_function	oxidoreductase activity
C	0016636	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
C	0016730	molecular_function	oxidoreductase activity, acting on iron-sulfur proteins as donors
C	0019685	biological_process	photosynthesis, dark reaction
C	0036068	biological_process	light-independent chlorophyll biosynthetic process
C	0046872	molecular_function	metal ion binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
D	0005524	molecular_function	ATP binding
D	0015979	biological_process	photosynthesis
D	0015995	biological_process	chlorophyll biosynthetic process
D	0016491	molecular_function	oxidoreductase activity
D	0016636	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
D	0016730	molecular_function	oxidoreductase activity, acting on iron-sulfur proteins as donors
D	0019685	biological_process	photosynthesis, dark reaction
D	0036068	biological_process	light-independent chlorophyll biosynthetic process
D	0046148	biological_process	pigment biosynthetic process
D	0046872	molecular_function	metal ion binding
D	0051539	molecular_function	4 iron, 4 sulfur cluster binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE 1PE A 1296

Chain	Residue
A	ALA196
A	LYS197
A	ASN198
A	TYR199
A	ARG202
D	LYS74
D	GLY110

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EPE A 1297

Chain	Residue
A	ALA212
A	GLU213
B	ASP236
B	ARG239
A	ASN177
A	SER211

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EPE B 1296

Chain	Residue
A	ASP236
A	ARG239
B	ASN177
B	SER211
B	ALA212
B	GLU213
B	HOH2041

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EPE A 1298

Chain	Residue
A	HIS69
A	THR82
A	ILE84
A	ASP85
A	GLY117
B	ASP286
B	ARG287
C	GLN334

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EPE D 1529

Chain	Residue
D	ARG180
D	ARG376
D	VAL388
D	ASP397
D	PRO399
D	ARG401
D	SER403
D	ASP417

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 1297

Chain	Residue
A	HOH2003
B	SER43
B	AF31298
B	ADP1299
B	HOH2004
B	HOH2005

site_id	AC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE AF3 A 1299

Chain	Residue
A	GLY38
A	GLY39
A	LYS42
A	ASP66
A	LYS68
A	GLY154
A	ADP1300
A	MG1301
A	HOH2006
A	HOH2008
A	HOH2009
A	HOH2010
A	HOH2019
B	LYS37
B	HOH2003

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 1530

Chain	Residue
C	HIS44
C	SER48
C	HOH2017
D	LEU42
D	MET393
D	HOH2044
D	HOH2045

site_id	AC9
Number of Residues	14
Details	BINDING SITE FOR RESIDUE AF3 B 1298

Chain	Residue
A	LYS37
A	HOH2003
A	HOH2005
A	HOH2046
B	GLY38
B	GLY39
B	LYS42
B	ASP66
B	LYS68
B	GLY154
B	MG1297
B	ADP1299
B	HOH2004
B	HOH2005

site_id	BC1
Number of Residues	22
Details	BINDING SITE FOR RESIDUE ADP A 1300

Chain	Residue
B	ASP180
A	GLY39
A	ILE40
A	GLY41
A	LYS42
A	SER43
A	THR44
A	ASN209
A	ARG210
A	ARG233
A	ASN234
A	VAL235
A	ILE238
A	ARG239
A	AF31299
A	MG1301
A	HOH2008
A	HOH2010
A	HOH2065
A	HOH2077
B	LYS37
B	ASP178

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 1301

Chain	Residue
A	SER43
A	AF31299
A	ADP1300
A	HOH2008
A	HOH2009
A	HOH2010

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE K D 1531

Chain	Residue
C	ARG40
D	GLU2
D	HOH2043

site_id	BC4
Number of Residues	22
Details	BINDING SITE FOR RESIDUE ADP B 1299

Chain	Residue
A	LYS37
A	ASP178
A	ASP180
A	GOL1303
A	HOH2003
A	HOH2058
B	GLY39
B	ILE40
B	GLY41
B	LYS42
B	SER43
B	THR44
B	ASN209
B	ARG210
B	ARG233
B	ASN234
B	VAL235
B	ILE238
B	ARG239
B	MG1297
B	AF31298
B	HOH2004

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 1412

Chain	Residue
C	PHE16
C	GLU293
C	GLY362
C	MET363
C	GLY364
C	HOH2004
C	HOH2005
C	HOH2086
D	THR37

site_id	BC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SF4 A 1302

Chain	Residue
A	CYS124
A	GLY125
A	GLY126
A	CYS158
A	HOH2089
B	CYS124
B	GLY125
B	GLY126
B	CYS158
C	VAL107
D	LEU99

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 C 1413

Chain	Residue
C	CYS17
C	LEU19
C	CYS42
C	SER102
C	CYS103
D	GLN34
D	ASP36
D	THR96

site_id	BC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL D 1532

Chain	Residue
A	GLN131
A	LYS134
D	GLU93
D	GLU98
D	GLN101
D	GLU121
D	LEU122
D	PRO123

site_id	BC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 1303

Chain	Residue
A	LYS37
A	GLY38
A	GLY39
A	ILE40
A	ASP178
A	SER181
B	GLY39
B	ADP1299

site_id	CC1
Number of Residues	24
Details	BINDING SITE FOR RESIDUE PMR C 1414

Chain	Residue
C	PHE16
C	THR20
C	VAL23
C	LEU45
C	SER48
C	ALA49
C	TRP378
C	ILE380
C	PHE384
C	HOH2019
C	HOH2101
C	HOH2102
C	HOH2103
D	TYR38
D	LEU41
D	LEU42
D	MET45
D	VAL289
D	ASP290
D	MET424
D	GLY425
D	LEU426
D	HIS429
D	HOH2075

Functional Information from PROSITE/UniProt

site_id	PS00692
Number of Residues	14
Details	NIFH_FRXC_2 NifH/frxC family signature 2. DvLGDVVCGGFAaP

Chain	Residue	Details
A	ASP151-PRO164

site_id	PS00746
Number of Residues	13
Details	NIFH_FRXC_1 NifH/frxC family signature 1. EsGGPpaGtGCGG

Chain	Residue	Details
A	GLU114-GLY126

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	ACT_SITE: Proton donor => ECO:0000255\|HAMAP-Rule:MF_00353

Chain	Residue	Details
D	ASP290
B	CYS124
B	CYS158
B	ASN209
C	CYS42
C	CYS103
A	CYS124
A	CYS158
A	ASN209
B	GLY39
B	SER43
B	LYS68

site_id	SWS_FT_FI2
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00353

Chain	Residue	Details
D	ASP36
D	GLY425

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