6VMK

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

Functional Information from GO Data

Chain	GOid	namespace	contents
C	0002376	biological_process	immune system process
C	0004252	molecular_function	serine-type endopeptidase activity
C	0005576	cellular_component	extracellular region
C	0005615	cellular_component	extracellular space
C	0006508	biological_process	proteolysis
C	0006956	biological_process	complement activation
C	0006957	biological_process	complement activation, alternative pathway
C	0008233	molecular_function	peptidase activity
C	0008236	molecular_function	serine-type peptidase activity
C	0016787	molecular_function	hydrolase activity
C	0031093	cellular_component	platelet alpha granule lumen
C	0031638	biological_process	zymogen activation
C	0034774	cellular_component	secretory granule lumen
C	0045087	biological_process	innate immune response
C	0051604	biological_process	protein maturation
C	0070062	cellular_component	extracellular exosome
C	1904813	cellular_component	ficolin-1-rich granule lumen
F	0002376	biological_process	immune system process
F	0004252	molecular_function	serine-type endopeptidase activity
F	0005576	cellular_component	extracellular region
F	0005615	cellular_component	extracellular space
F	0006508	biological_process	proteolysis
F	0006956	biological_process	complement activation
F	0006957	biological_process	complement activation, alternative pathway
F	0008233	molecular_function	peptidase activity
F	0008236	molecular_function	serine-type peptidase activity
F	0016787	molecular_function	hydrolase activity
F	0031093	cellular_component	platelet alpha granule lumen
F	0031638	biological_process	zymogen activation
F	0034774	cellular_component	secretory granule lumen
F	0045087	biological_process	innate immune response
F	0051604	biological_process	protein maturation
F	0070062	cellular_component	extracellular exosome
F	1904813	cellular_component	ficolin-1-rich granule lumen
I	0002376	biological_process	immune system process
I	0004252	molecular_function	serine-type endopeptidase activity
I	0005576	cellular_component	extracellular region
I	0005615	cellular_component	extracellular space
I	0006508	biological_process	proteolysis
I	0006956	biological_process	complement activation
I	0006957	biological_process	complement activation, alternative pathway
I	0008233	molecular_function	peptidase activity
I	0008236	molecular_function	serine-type peptidase activity
I	0016787	molecular_function	hydrolase activity
I	0031093	cellular_component	platelet alpha granule lumen
I	0031638	biological_process	zymogen activation
I	0034774	cellular_component	secretory granule lumen
I	0045087	biological_process	innate immune response
I	0051604	biological_process	protein maturation
I	0070062	cellular_component	extracellular exosome
I	1904813	cellular_component	ficolin-1-rich granule lumen
N	0002376	biological_process	immune system process
N	0004252	molecular_function	serine-type endopeptidase activity
N	0005576	cellular_component	extracellular region
N	0005615	cellular_component	extracellular space
N	0006508	biological_process	proteolysis
N	0006956	biological_process	complement activation
N	0006957	biological_process	complement activation, alternative pathway
N	0008233	molecular_function	peptidase activity
N	0008236	molecular_function	serine-type peptidase activity
N	0016787	molecular_function	hydrolase activity
N	0031093	cellular_component	platelet alpha granule lumen
N	0031638	biological_process	zymogen activation
N	0034774	cellular_component	secretory granule lumen
N	0045087	biological_process	innate immune response
N	0051604	biological_process	protein maturation
N	0070062	cellular_component	extracellular exosome
N	1904813	cellular_component	ficolin-1-rich granule lumen
Q	0002376	biological_process	immune system process
Q	0004252	molecular_function	serine-type endopeptidase activity
Q	0005576	cellular_component	extracellular region
Q	0005615	cellular_component	extracellular space
Q	0006508	biological_process	proteolysis
Q	0006956	biological_process	complement activation
Q	0006957	biological_process	complement activation, alternative pathway
Q	0008233	molecular_function	peptidase activity
Q	0008236	molecular_function	serine-type peptidase activity
Q	0016787	molecular_function	hydrolase activity
Q	0031093	cellular_component	platelet alpha granule lumen
Q	0031638	biological_process	zymogen activation
Q	0034774	cellular_component	secretory granule lumen
Q	0045087	biological_process	innate immune response
Q	0051604	biological_process	protein maturation
Q	0070062	cellular_component	extracellular exosome
Q	1904813	cellular_component	ficolin-1-rich granule lumen
T	0002376	biological_process	immune system process
T	0004252	molecular_function	serine-type endopeptidase activity
T	0005576	cellular_component	extracellular region
T	0005615	cellular_component	extracellular space
T	0006508	biological_process	proteolysis
T	0006956	biological_process	complement activation
T	0006957	biological_process	complement activation, alternative pathway
T	0008233	molecular_function	peptidase activity
T	0008236	molecular_function	serine-type peptidase activity
T	0016787	molecular_function	hydrolase activity
T	0031093	cellular_component	platelet alpha granule lumen
T	0031638	biological_process	zymogen activation
T	0034774	cellular_component	secretory granule lumen
T	0045087	biological_process	innate immune response
T	0051604	biological_process	protein maturation
T	0070062	cellular_component	extracellular exosome
T	1904813	cellular_component	ficolin-1-rich granule lumen
W	0002376	biological_process	immune system process
W	0004252	molecular_function	serine-type endopeptidase activity
W	0005576	cellular_component	extracellular region
W	0005615	cellular_component	extracellular space
W	0006508	biological_process	proteolysis
W	0006956	biological_process	complement activation
W	0006957	biological_process	complement activation, alternative pathway
W	0008233	molecular_function	peptidase activity
W	0008236	molecular_function	serine-type peptidase activity
W	0016787	molecular_function	hydrolase activity
W	0031093	cellular_component	platelet alpha granule lumen
W	0031638	biological_process	zymogen activation
W	0034774	cellular_component	secretory granule lumen
W	0045087	biological_process	innate immune response
W	0051604	biological_process	protein maturation
W	0070062	cellular_component	extracellular exosome
W	1904813	cellular_component	ficolin-1-rich granule lumen
X	0002376	biological_process	immune system process
X	0004252	molecular_function	serine-type endopeptidase activity
X	0005576	cellular_component	extracellular region
X	0005615	cellular_component	extracellular space
X	0006508	biological_process	proteolysis
X	0006956	biological_process	complement activation
X	0006957	biological_process	complement activation, alternative pathway
X	0008233	molecular_function	peptidase activity
X	0008236	molecular_function	serine-type peptidase activity
X	0016787	molecular_function	hydrolase activity
X	0031093	cellular_component	platelet alpha granule lumen
X	0031638	biological_process	zymogen activation
X	0034774	cellular_component	secretory granule lumen
X	0045087	biological_process	innate immune response
X	0051604	biological_process	protein maturation
X	0070062	cellular_component	extracellular exosome
X	1904813	cellular_component	ficolin-1-rich granule lumen
a	0002376	biological_process	immune system process
a	0004252	molecular_function	serine-type endopeptidase activity
a	0005576	cellular_component	extracellular region
a	0005615	cellular_component	extracellular space
a	0006508	biological_process	proteolysis
a	0006956	biological_process	complement activation
a	0006957	biological_process	complement activation, alternative pathway
a	0008233	molecular_function	peptidase activity
a	0008236	molecular_function	serine-type peptidase activity
a	0016787	molecular_function	hydrolase activity
a	0031093	cellular_component	platelet alpha granule lumen
a	0031638	biological_process	zymogen activation
a	0034774	cellular_component	secretory granule lumen
a	0045087	biological_process	innate immune response
a	0051604	biological_process	protein maturation
a	0070062	cellular_component	extracellular exosome
a	1904813	cellular_component	ficolin-1-rich granule lumen
d	0002376	biological_process	immune system process
d	0004252	molecular_function	serine-type endopeptidase activity
d	0005576	cellular_component	extracellular region
d	0005615	cellular_component	extracellular space
d	0006508	biological_process	proteolysis
d	0006956	biological_process	complement activation
d	0006957	biological_process	complement activation, alternative pathway
d	0008233	molecular_function	peptidase activity
d	0008236	molecular_function	serine-type peptidase activity
d	0016787	molecular_function	hydrolase activity
d	0031093	cellular_component	platelet alpha granule lumen
d	0031638	biological_process	zymogen activation
d	0034774	cellular_component	secretory granule lumen
d	0045087	biological_process	innate immune response
d	0051604	biological_process	protein maturation
d	0070062	cellular_component	extracellular exosome
d	1904813	cellular_component	ficolin-1-rich granule lumen
g	0002376	biological_process	immune system process
g	0004252	molecular_function	serine-type endopeptidase activity
g	0005576	cellular_component	extracellular region
g	0005615	cellular_component	extracellular space
g	0006508	biological_process	proteolysis
g	0006956	biological_process	complement activation
g	0006957	biological_process	complement activation, alternative pathway
g	0008233	molecular_function	peptidase activity
g	0008236	molecular_function	serine-type peptidase activity
g	0016787	molecular_function	hydrolase activity
g	0031093	cellular_component	platelet alpha granule lumen
g	0031638	biological_process	zymogen activation
g	0034774	cellular_component	secretory granule lumen
g	0045087	biological_process	innate immune response
g	0051604	biological_process	protein maturation
g	0070062	cellular_component	extracellular exosome
g	1904813	cellular_component	ficolin-1-rich granule lumen
j	0002376	biological_process	immune system process
j	0004252	molecular_function	serine-type endopeptidase activity
j	0005576	cellular_component	extracellular region
j	0005615	cellular_component	extracellular space
j	0006508	biological_process	proteolysis
j	0006956	biological_process	complement activation
j	0006957	biological_process	complement activation, alternative pathway
j	0008233	molecular_function	peptidase activity
j	0008236	molecular_function	serine-type peptidase activity
j	0016787	molecular_function	hydrolase activity
j	0031093	cellular_component	platelet alpha granule lumen
j	0031638	biological_process	zymogen activation
j	0034774	cellular_component	secretory granule lumen
j	0045087	biological_process	innate immune response
j	0051604	biological_process	protein maturation
j	0070062	cellular_component	extracellular exosome
j	1904813	cellular_component	ficolin-1-rich granule lumen
m	0002376	biological_process	immune system process
m	0004252	molecular_function	serine-type endopeptidase activity
m	0005576	cellular_component	extracellular region
m	0005615	cellular_component	extracellular space
m	0006508	biological_process	proteolysis
m	0006956	biological_process	complement activation
m	0006957	biological_process	complement activation, alternative pathway
m	0008233	molecular_function	peptidase activity
m	0008236	molecular_function	serine-type peptidase activity
m	0016787	molecular_function	hydrolase activity
m	0031093	cellular_component	platelet alpha granule lumen
m	0031638	biological_process	zymogen activation
m	0034774	cellular_component	secretory granule lumen
m	0045087	biological_process	innate immune response
m	0051604	biological_process	protein maturation
m	0070062	cellular_component	extracellular exosome
m	1904813	cellular_component	ficolin-1-rich granule lumen
p	0002376	biological_process	immune system process
p	0004252	molecular_function	serine-type endopeptidase activity
p	0005576	cellular_component	extracellular region
p	0005615	cellular_component	extracellular space
p	0006508	biological_process	proteolysis
p	0006956	biological_process	complement activation
p	0006957	biological_process	complement activation, alternative pathway
p	0008233	molecular_function	peptidase activity
p	0008236	molecular_function	serine-type peptidase activity
p	0016787	molecular_function	hydrolase activity
p	0031093	cellular_component	platelet alpha granule lumen
p	0031638	biological_process	zymogen activation
p	0034774	cellular_component	secretory granule lumen
p	0045087	biological_process	innate immune response
p	0051604	biological_process	protein maturation
p	0070062	cellular_component	extracellular exosome
p	1904813	cellular_component	ficolin-1-rich granule lumen
s	0002376	biological_process	immune system process
s	0004252	molecular_function	serine-type endopeptidase activity
s	0005576	cellular_component	extracellular region
s	0005615	cellular_component	extracellular space
s	0006508	biological_process	proteolysis
s	0006956	biological_process	complement activation
s	0006957	biological_process	complement activation, alternative pathway
s	0008233	molecular_function	peptidase activity
s	0008236	molecular_function	serine-type peptidase activity
s	0016787	molecular_function	hydrolase activity
s	0031093	cellular_component	platelet alpha granule lumen
s	0031638	biological_process	zymogen activation
s	0034774	cellular_component	secretory granule lumen
s	0045087	biological_process	innate immune response
s	0051604	biological_process	protein maturation
s	0070062	cellular_component	extracellular exosome
s	1904813	cellular_component	ficolin-1-rich granule lumen
v	0002376	biological_process	immune system process
v	0004252	molecular_function	serine-type endopeptidase activity
v	0005576	cellular_component	extracellular region
v	0005615	cellular_component	extracellular space
v	0006508	biological_process	proteolysis
v	0006956	biological_process	complement activation
v	0006957	biological_process	complement activation, alternative pathway
v	0008233	molecular_function	peptidase activity
v	0008236	molecular_function	serine-type peptidase activity
v	0016787	molecular_function	hydrolase activity
v	0031093	cellular_component	platelet alpha granule lumen
v	0031638	biological_process	zymogen activation
v	0034774	cellular_component	secretory granule lumen
v	0045087	biological_process	innate immune response
v	0051604	biological_process	protein maturation
v	0070062	cellular_component	extracellular exosome
v	1904813	cellular_component	ficolin-1-rich granule lumen

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue GOL W 301

Chain	Residue
W	HIS57
W	GLY193
W	SER195

---

site_id	AC2
Number of Residues	5
Details	binding site for residue SO4 W 302

Chain	Residue
M	LYS19
M	GLU82
W	ARG20
W	GLU21
W	HIS157

---

site_id	AC3
Number of Residues	2
Details	binding site for residue GOL C 301

Chain	Residue
C	SER195
C	HIS57

---

site_id	AC4
Number of Residues	5
Details	binding site for residue SO4 C 302

Chain	Residue
B	LYS19
B	GLU82
C	ARG20
C	GLU23
C	HIS157

---

site_id	AC5
Number of Residues	4
Details	binding site for residue GOL F 301

Chain	Residue
F	HIS57
F	GLY193
F	SER195
F	HOH425

---

site_id	AC6
Number of Residues	2
Details	binding site for residue GOL I 301

Chain	Residue
I	GLY193
I	SER195

---

site_id	AC7
Number of Residues	3
Details	binding site for residue GOL N 301

Chain	Residue
N	HIS57
N	GLY193
N	SER195

---

site_id	AC8
Number of Residues	5
Details	binding site for residue SO4 N 302

Chain	Residue
N	ARG20
N	GLU23
N	HIS157
N	HOH401
N	HOH402

---

site_id	AC9
Number of Residues	4
Details	binding site for residue GOL Q 301

Chain	Residue
Q	LYS192
Q	GLY193
Q	SER195
Q	GLY216

---

site_id	AD1
Number of Residues	2
Details	binding site for residue SO4 Q 302

Chain	Residue
Q	ARG20
Q	HIS157

---

site_id	AD2
Number of Residues	3
Details	binding site for residue GOL T 301

Chain	Residue
T	HIS57
T	GLY193
T	SER195

---

site_id	AD3
Number of Residues	3
Details	binding site for residue SO4 T 302

Chain	Residue
T	ARG20
T	GLU21
T	HIS157

---

site_id	AD4
Number of Residues	6
Details	binding site for residue GOL X 301

Chain	Residue
X	CYS42
X	HIS57
X	LYS192
X	GLY193
X	SER195
X	GLY216

---

site_id	AD5
Number of Residues	4
Details	binding site for residue SO4 X 302

Chain	Residue
X	ARG20
X	GLU21
X	HIS157
X	HOH401

---

site_id	AD6
Number of Residues	4
Details	binding site for residue GOL a 301

Chain	Residue
a	HIS57
a	GLY193
a	SER195
a	HOH436

---

site_id	AD7
Number of Residues	5
Details	binding site for residue GOL d 301

Chain	Residue
d	CYS42
d	HIS57
d	GLY193
d	SER195
d	HOH406

---

site_id	AD8
Number of Residues	3
Details	binding site for residue GOL g 301

Chain	Residue
g	HIS57
g	GLY193
g	SER195

---

site_id	AD9
Number of Residues	2
Details	binding site for residue SO4 g 302

Chain	Residue
g	ARG20
g	HIS157

---

site_id	AE1
Number of Residues	6
Details	binding site for residue GOL j 301

Chain	Residue
j	LEU41
j	HIS57
j	LYS192
j	GLY193
j	SER195
j	HOH403

---

site_id	AE2
Number of Residues	2
Details	binding site for residue SO4 j 302

Chain	Residue
j	GLU21
j	HIS157

---

site_id	AE3
Number of Residues	4
Details	binding site for residue GOL m 301

Chain	Residue
m	HIS57
m	GLY193
m	SER195
m	GLY216

---

site_id	AE4
Number of Residues	2
Details	binding site for residue SO4 m 302

Chain	Residue
m	ARG20
m	HIS157

---

site_id	AE5
Number of Residues	5
Details	binding site for residue GOL p 301

Chain	Residue
p	CYS42
p	HIS57
p	GLY193
p	SER195
p	HOH405

---

site_id	AE6
Number of Residues	2
Details	binding site for residue SO4 p 302

Chain	Residue
p	ARG20
p	HIS157

---

site_id	AE7
Number of Residues	3
Details	binding site for residue GOL s 301

Chain	Residue
s	CYS42
s	HIS57
s	SER195

---

site_id	AE8
Number of Residues	3
Details	binding site for residue SO4 s 302

Chain	Residue
s	ARG20
s	GLU23
s	HIS157

---

site_id	AE9
Number of Residues	3
Details	binding site for residue GOL v 301

Chain	Residue
v	GLY193
v	SER195
v	GLY216

---

site_id	AF1
Number of Residues	2
Details	binding site for residue SO4 v 302

Chain	Residue
v	ARG20
v	HIS157

---

Functional Information from PROSITE/UniProt

site_id	PS00134
Number of Residues	6
Details	TRYPSIN_HIS Serine proteases, trypsin family, histidine active site. LSAAHC

Chain	Residue	Details
W	LEU53-CYS58

---

site_id	PS00135
Number of Residues	12
Details	TRYPSIN_SER Serine proteases, trypsin family, serine active site. DSckGDSGGPLV

Chain	Residue	Details
W	ASP189-VAL200

---

site_id	PS00290
Number of Residues	7
Details	IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YACEVTH

Chain	Residue	Details
L	TYR192-HIS198
Z	TYR196-HIS202

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3632
Details	Domain: {"description":"Peptidase S1","evidences":[{"source":"PROSITE-ProRule","id":"PRU00274","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	64
Details	Region: {"description":"Self-inhibitor loop","evidences":[{"source":"PubMed","id":"10022823","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9753554","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	16
Details	Active site: {"description":"Charge relay system","evidences":[{"source":"PubMed","id":"7592653","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9753554","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	16
Details	Active site: {"description":"Charge relay system","evidences":[{"source":"PubMed","id":"7592653","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	16
Details	Active site: {"description":"Charge relay system","evidences":[{"source":"PubMed","id":"7592653","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21205667","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"22362762","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---