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3QUM
Asym. Unit
Info
Asym.Unit (372 KB)
Biol.Unit 1 (186 KB)
Biol.Unit 2 (185 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PROSTATE SPECIFIC ANTIGEN (PSA) IN FAB SANDWICH WITH A HIGH AFFINITY AND A PCA SELECTIVE ANTIBODY
Authors
:
E. A. Stura, B. H. Muller, S. Michel, F. Ducancel
Date
:
24 Feb 11 (Deposition) - 09 Nov 11 (Release) - 21 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,H,K,L,M,P,Q
Biol. Unit 1: A,B,H,L,P (1x)
Biol. Unit 2: C,D,K,M,Q (1x)
Keywords
:
Kallikrein Fold, Prostate-Specific Antigen, Serine Protease, Negative Regulation Of Angiogenesis, Natural Post-Transductional Modification, N-Linked And O-Linked Glycosylation, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. A. Stura, B. H. Muller, M. Bossus, S. Michel, C. Jolivet-Reynaud, F. Ducancel
Crystal Structure Of Human Prostate-Specific Antigen In A Sandwich Antibody Complex.
J. Mol. Biol. V. 414 530 2011
(for further references see the
PDB file header
)
[
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Hetero Components
(6, 32)
Info
All Hetero Components
1a: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ga)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
3d: BETA-D-GALACTOSE (GALd)
3e: BETA-D-GALACTOSE (GALe)
3f: BETA-D-GALACTOSE (GALf)
3g: BETA-D-GALACTOSE (GALg)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6a: O-SIALIC ACID (SIAa)
6b: O-SIALIC ACID (SIAb)
6c: O-SIALIC ACID (SIAc)
6d: O-SIALIC ACID (SIAd)
6e: O-SIALIC ACID (SIAe)
6f: O-SIALIC ACID (SIAf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A2G
1
Ligand/Ion
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
3
GAL
7
Ligand/Ion
BETA-D-GALACTOSE
4
MAN
6
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SIA
6
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(32, 32)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR B:56 , ILE P:59 , ARG P:60 , ASN P:61 , NAG P:402 , FUC P:415
BINDING SITE FOR RESIDUE NAG P 401
02
AC2
SOFTWARE
NAG P:401 , MAN P:403 , NAG P:412 , FUC P:415
BINDING SITE FOR RESIDUE NAG P 402
03
AC3
SOFTWARE
HOH P:265 , NAG P:402 , MAN P:404 , MAN P:411 , NAG P:412
BINDING SITE FOR RESIDUE MAN P 403
04
AC4
SOFTWARE
MAN P:403 , NAG P:405 , NAG P:408
BINDING SITE FOR RESIDUE MAN P 404
05
AC5
SOFTWARE
MAN P:404 , GAL P:406 , NAG P:408
BINDING SITE FOR RESIDUE NAG P 405
06
AC6
SOFTWARE
LYS B:64 , NAG P:405 , SIA P:407 , SIA P:414
BINDING SITE FOR RESIDUE GAL P 406
07
AC7
SOFTWARE
GLN B:61 , LYS B:64 , HOH P:268 , GAL P:406
BINDING SITE FOR RESIDUE SIA P 407
08
AC8
SOFTWARE
MAN P:404 , NAG P:405 , GAL P:409
BINDING SITE FOR RESIDUE NAG P 408
09
AC9
SOFTWARE
NAG P:408 , SIA P:410
BINDING SITE FOR RESIDUE GAL P 409
10
BC1
SOFTWARE
GLN B:3 , GLN B:5 , LYS B:23 , SER B:25 , GAL P:409
BINDING SITE FOR RESIDUE SIA P 410
11
BC2
SOFTWARE
MAN P:403 , NAG P:412
BINDING SITE FOR RESIDUE MAN P 411
12
BC3
SOFTWARE
NAG P:402 , MAN P:403 , MAN P:411 , GAL P:413 , FUC P:415
BINDING SITE FOR RESIDUE NAG P 412
13
BC4
SOFTWARE
HOH P:268 , NAG P:412 , SIA P:414
BINDING SITE FOR RESIDUE GAL P 413
14
BC5
SOFTWARE
GAL P:406 , GAL P:413
BINDING SITE FOR RESIDUE SIA P 414
15
BC6
SOFTWARE
TYR B:56 , NAG P:401 , NAG P:402 , NAG P:412
BINDING SITE FOR RESIDUE FUC P 415
16
BC7
SOFTWARE
PRO P:124 , THR P:125 , GLN P:128 , VAL P:208 , HOH P:247 , GAL P:301
BINDING SITE FOR RESIDUE A2G P 300
17
BC8
SOFTWARE
ALA H:28 , ILE H:29 , SER H:30 , LYS H:73 , A2G P:300
BINDING SITE FOR RESIDUE GAL P 301
18
BC9
SOFTWARE
ILE Q:59 , ARG Q:60 , ASN Q:61 , NAG Q:402 , FUC Q:415
BINDING SITE FOR RESIDUE NAG Q 401
19
CC1
SOFTWARE
NAG Q:401 , MAN Q:403
BINDING SITE FOR RESIDUE NAG Q 402
20
CC2
SOFTWARE
NAG Q:402 , MAN Q:404 , MAN Q:411
BINDING SITE FOR RESIDUE MAN Q 403
21
CC3
SOFTWARE
MAN Q:403 , NAG Q:405 , NAG Q:408 , SIA Q:410
BINDING SITE FOR RESIDUE MAN Q 404
22
CC4
SOFTWARE
MAN Q:404 , GAL Q:406 , GAL Q:409 , SIA Q:410
BINDING SITE FOR RESIDUE NAG Q 405
23
CC5
SOFTWARE
NAG Q:405 , SIA Q:407 , SIA Q:410
BINDING SITE FOR RESIDUE GAL Q 406
24
CC6
SOFTWARE
GAL Q:406
BINDING SITE FOR RESIDUE SIA Q 407
25
CC7
SOFTWARE
MAN Q:404 , GAL Q:409
BINDING SITE FOR RESIDUE NAG Q 408
26
CC8
SOFTWARE
NAG Q:405 , NAG Q:408 , SIA Q:410
BINDING SITE FOR RESIDUE GAL Q 409
27
CC9
SOFTWARE
LYS Q:95E , ASN Q:95F , PHE Q:95H , MAN Q:404 , NAG Q:405 , GAL Q:406 , GAL Q:409
BINDING SITE FOR RESIDUE SIA Q 410
28
DC1
SOFTWARE
MAN Q:403 , NAG Q:412
BINDING SITE FOR RESIDUE MAN Q 411
29
DC2
SOFTWARE
MAN Q:411 , GAL Q:413 , SIA Q:414
BINDING SITE FOR RESIDUE NAG Q 412
30
DC3
SOFTWARE
NAG Q:412 , SIA Q:414
BINDING SITE FOR RESIDUE GAL Q 413
31
DC4
SOFTWARE
NAG Q:412 , GAL Q:413
BINDING SITE FOR RESIDUE SIA Q 414
32
DC5
SOFTWARE
TYR D:56 , NAG Q:401
BINDING SITE FOR RESIDUE FUC Q 415
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_021941 (E23K, chain P/Q, )
2: VAR_021942 (L114I, chain P/Q, )
3: VAR_051852 (I163T, chain P/Q, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021941
E
32
K
KLK3_HUMAN
Polymorphism
2271092
P/Q
E
23
K
2
UniProt
VAR_021942
L
132
I
KLK3_HUMAN
Polymorphism
2003783
P/Q
L
114
I
3
UniProt
VAR_051852
I
179
T
KLK3_HUMAN
Polymorphism
17632542
P/Q
I
163
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (P:16-243,Q:16-243)
2: TRYPSIN_HIS (P:53-58,Q:53-58)
3: TRYPSIN_SER (P:189-200,Q:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
KLK3_HUMAN
25-258
2
P:16-243
Q:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
KLK3_HUMAN
61-66
2
P:53-58
Q:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
KLK3_HUMAN
207-218
2
P:189-200
Q:189-200
[
close PROSITE info
]
Exons
(4, 8)
Info
All Exons
Exon 1.2a (P:16-61 (gaps) | Q:16-61 (gaps))
Exon 1.3b (P:61-149 (gaps) | Q:61-149 (gaps))
Exon 1.4 (P:149-192 | Q:149-192)
Exon 1.5b (P:193-246 (gaps) | Q:193-246 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2a
2: Boundary 1.2a/1.3b
3: Boundary 1.3b/1.4
4: Boundary 1.4/1.5b
5: Boundary 1.5b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000326003
1
ENSE00001123926
chr19:
51358171-51358257
87
KLK3_HUMAN
1-16
16
0
-
-
1.2a
ENST00000326003
2a
ENSE00001718125
chr19:
51359496-51359655
160
KLK3_HUMAN
16-69
54
2
P:16-61 (gaps)
Q:16-61 (gaps)
46
46
1.3b
ENST00000326003
3b
ENSE00001268279
chr19:
51361285-51361571
287
KLK3_HUMAN
69-165
97
2
P:61-149 (gaps)
Q:61-149 (gaps)
100
100
1.4
ENST00000326003
4
ENSE00001268316
chr19:
51361715-51361851
137
KLK3_HUMAN
165-210
46
2
P:149-192
Q:149-192
46
46
1.5b
ENST00000326003
5b
ENSE00001268296
chr19:
51363228-51364020
793
KLK3_HUMAN
211-261
51
2
P:193-246 (gaps)
Q:193-246 (gaps)
55
55
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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