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2XE4
Asym. Unit
Info
Asym.Unit (310 KB)
Biol.Unit 1 (300 KB)
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(1)
Title
:
STRUCTURE OF OLIGOPEPTIDASE B FROM LEISHMANIA MAJOR
Authors
:
K. Mcluskey, N. G. Paterson, N. D. Bland, J. C. Mottram, N. W. Isaacs
Date
:
11 May 10 (Deposition) - 06 Oct 10 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase-Inhibitor Complex, Hydrolase, Protease Inhibitor Trypanosomes, Clan Sc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Mcluskey, N. G. Paterson, N. D. Bland, N. W. Isaacs, J. C. Mottram
Crystal Structure Of Leishmania Major Oligopeptidase B Gives Insight Into The Enzymatic Properties Of A Trypanosomatid Virulence Factor.
J. Biol. Chem. V. 285 39249 2010
[
close entry info
]
Hetero Components
(8, 70)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: N-CARBOXY-L-PHENYLALANINE (FC0a)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: S-1,2-PROPANEDIOL (PGOa)
6a: R-1,2-PROPANEDIOL (PGRa)
6aa: R-1,2-PROPANEDIOL (PGRaa)
6ab: R-1,2-PROPANEDIOL (PGRab)
6ac: R-1,2-PROPANEDIOL (PGRac)
6ad: R-1,2-PROPANEDIOL (PGRad)
6ae: R-1,2-PROPANEDIOL (PGRae)
6af: R-1,2-PROPANEDIOL (PGRaf)
6ag: R-1,2-PROPANEDIOL (PGRag)
6ah: R-1,2-PROPANEDIOL (PGRah)
6ai: R-1,2-PROPANEDIOL (PGRai)
6aj: R-1,2-PROPANEDIOL (PGRaj)
6ak: R-1,2-PROPANEDIOL (PGRak)
6al: R-1,2-PROPANEDIOL (PGRal)
6am: R-1,2-PROPANEDIOL (PGRam)
6an: R-1,2-PROPANEDIOL (PGRan)
6ao: R-1,2-PROPANEDIOL (PGRao)
6ap: R-1,2-PROPANEDIOL (PGRap)
6aq: R-1,2-PROPANEDIOL (PGRaq)
6ar: R-1,2-PROPANEDIOL (PGRar)
6as: R-1,2-PROPANEDIOL (PGRas)
6at: R-1,2-PROPANEDIOL (PGRat)
6au: R-1,2-PROPANEDIOL (PGRau)
6av: R-1,2-PROPANEDIOL (PGRav)
6b: R-1,2-PROPANEDIOL (PGRb)
6c: R-1,2-PROPANEDIOL (PGRc)
6d: R-1,2-PROPANEDIOL (PGRd)
6e: R-1,2-PROPANEDIOL (PGRe)
6f: R-1,2-PROPANEDIOL (PGRf)
6g: R-1,2-PROPANEDIOL (PGRg)
6h: R-1,2-PROPANEDIOL (PGRh)
6i: R-1,2-PROPANEDIOL (PGRi)
6j: R-1,2-PROPANEDIOL (PGRj)
6k: R-1,2-PROPANEDIOL (PGRk)
6l: R-1,2-PROPANEDIOL (PGRl)
6m: R-1,2-PROPANEDIOL (PGRm)
6n: R-1,2-PROPANEDIOL (PGRn)
6o: R-1,2-PROPANEDIOL (PGRo)
6p: R-1,2-PROPANEDIOL (PGRp)
6q: R-1,2-PROPANEDIOL (PGRq)
6r: R-1,2-PROPANEDIOL (PGRr)
6s: R-1,2-PROPANEDIOL (PGRs)
6t: R-1,2-PROPANEDIOL (PGRt)
6u: R-1,2-PROPANEDIOL (PGRu)
6v: R-1,2-PROPANEDIOL (PGRv)
6w: R-1,2-PROPANEDIOL (PGRw)
6x: R-1,2-PROPANEDIOL (PGRx)
6y: R-1,2-PROPANEDIOL (PGRy)
6z: R-1,2-PROPANEDIOL (PGRz)
7a: PHOSPHATE ION (PO4a)
7b: PHOSPHATE ION (PO4b)
7c: PHOSPHATE ION (PO4c)
8a: ARGINAL (RGLa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
FC0
1
Mod. Amino Acid
N-CARBOXY-L-PHENYLALANINE
3
GOL
10
Ligand/Ion
GLYCEROL
4
NA
2
Ligand/Ion
SODIUM ION
5
PGO
1
Ligand/Ion
S-1,2-PROPANEDIOL
6
PGR
48
Ligand/Ion
R-1,2-PROPANEDIOL
7
PO4
3
Ligand/Ion
PHOSPHATE ION
8
RGL
1
Mod. Amino Acid
ARGINAL
[
close Hetero Component info
]
Sites
(69, 69)
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)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
59: GC5 (SOFTWARE)
60: GC6 (SOFTWARE)
61: GC7 (SOFTWARE)
62: GC8 (SOFTWARE)
63: GC9 (SOFTWARE)
64: HC1 (SOFTWARE)
65: HC2 (SOFTWARE)
66: HC3 (SOFTWARE)
67: HC4 (SOFTWARE)
68: HC5 (SOFTWARE)
69: HC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:591 , ASP A:592 , PHE A:594 , GLU A:650 , TYR A:651 , PRO A:652 , PGR A:1766 , HOH A:2610 , HOH A:2710
BINDING SITE FOR RESIDUE GOL A1732
02
AC2
SOFTWARE
HIS A:340 , VAL A:341 , PHE A:385 , LYS A:386 , ALA A:387 , PGR A:1759
BINDING SITE FOR RESIDUE GOL A1733
03
AC3
SOFTWARE
GLY A:452 , HIS A:480 , ASP A:516 , ARG A:726 , LEU A:727 , LEU A:728 , HOH A:2479 , HOH A:2682
BINDING SITE FOR RESIDUE GOL A1734
04
AC4
SOFTWARE
LYS A:595 , ASN A:653 , ASN A:685 , HIS A:720 , PGR A:1767
BINDING SITE FOR RESIDUE GOL A1735
05
AC5
SOFTWARE
PHE A:698 , HOH A:2720
BINDING SITE FOR RESIDUE GOL A1736
06
AC6
SOFTWARE
GLN A:437 , HIS A:439 , HOH A:2683
BINDING SITE FOR RESIDUE GOL A1737
07
AC7
SOFTWARE
SER A:311 , VAL A:446 , ARG A:447 , GLU A:448 , VAL A:449 , HOH A:2362 , HOH A:2684 , HOH A:2685
BINDING SITE FOR RESIDUE GOL A1738
08
AC8
SOFTWARE
THR A:466 , ALA A:555 , GLU A:558
BINDING SITE FOR RESIDUE GOL A1739
09
AC9
SOFTWARE
ARG A:547 , SER A:551 , MET A:589 , ASP A:635 , TYR A:636 , HOH A:2546 , HOH A:2590 , HOH A:2591
BINDING SITE FOR RESIDUE GOL A1740
10
BC1
SOFTWARE
LYS A:299 , TYR A:543 , TRP A:622 , ASN A:627 , TYR A:633 , HOH A:2587 , HOH A:2686 , HOH A:2687
BINDING SITE FOR RESIDUE GOL A1741
11
BC2
SOFTWARE
GLU A:574 , GLY A:575 , GLY A:600 , GLN A:713 , PGO A:1743 , HOH A:2688 , HOH A:2706
BINDING SITE FOR RESIDUE PGR A1742
12
BC3
SOFTWARE
GLN A:510 , TYR A:514 , GLU A:574 , LEU A:598 , SER A:710 , PGR A:1742 , PGR A:1777
BINDING SITE FOR RESIDUE PGO A1743
13
BC4
SOFTWARE
HIS A:308 , GLY A:309 , SER A:311 , HIS A:312 , ASP A:454 , HOH A:2441
BINDING SITE FOR RESIDUE PGR A1744
14
BC5
SOFTWARE
ALA A:700 , LYS A:701 , ARG A:703 , PHE A:706 , HOH A:2162 , HOH A:2656
BINDING SITE FOR RESIDUE PGR A1745
15
BC6
SOFTWARE
TRP A:50 , ARG A:52 , ASP A:53 , PGR A:1775 , PGR A:1780 , HOH A:2091 , HOH A:2691 , HOH A:2700
BINDING SITE FOR RESIDUE PGR A1746
16
BC7
SOFTWARE
ARG A:527 , ALA A:535 , GLY A:540 , HOH A:2491 , HOH A:2692
BINDING SITE FOR RESIDUE PGR A1747
17
BC8
SOFTWARE
ASP A:155 , MET A:157 , PHE A:698 , LYS A:701 , HOH A:2195 , HOH A:2693
BINDING SITE FOR RESIDUE PGR A1748
18
BC9
SOFTWARE
GLY A:369 , ARG A:462 , PRO A:474 , SER A:476 , HIS A:525 , HOH A:2716
BINDING SITE FOR RESIDUE PGR A1749
19
CC1
SOFTWARE
ALA A:88 , GLU A:89 , SER A:92 , GLY A:451 , HOH A:2674
BINDING SITE FOR RESIDUE PGR A1750
20
CC2
SOFTWARE
TYR A:103 , TYR A:110 , VAL A:159 , LEU A:411
BINDING SITE FOR RESIDUE PGR A1751
21
CC3
SOFTWARE
ILE A:142 , ASP A:143 , LYS A:186 , HOH A:2694
BINDING SITE FOR RESIDUE PGR A1752
22
CC4
SOFTWARE
ALA A:259 , LEU A:411 , HOH A:2152 , HOH A:2204 , HOH A:2437
BINDING SITE FOR RESIDUE PGR A1753
23
CC5
SOFTWARE
THR A:262 , ASN A:263 , LEU A:282
BINDING SITE FOR RESIDUE PGR A1754
24
CC6
SOFTWARE
GLY A:300 , VAL A:301 , ASN A:318 , GLY A:320 , GLY A:321 , HOH A:2357
BINDING SITE FOR RESIDUE PGR A1755
25
CC7
SOFTWARE
ARG A:302 , ASP A:304 , LEU A:316 , HIS A:325 , HOH A:2385
BINDING SITE FOR RESIDUE PGR A1756
26
CC8
SOFTWARE
ASP A:261 , ASP A:454 , ASN A:457 , LYS A:481 , HOH A:2311 , HOH A:2442 , HOH A:2695
BINDING SITE FOR RESIDUE PGR A1757
27
CC9
SOFTWARE
ASP A:281 , ARG A:283 , ARG A:332 , THR A:427 , HOH A:2696
BINDING SITE FOR RESIDUE PGR A1758
28
DC1
SOFTWARE
HIS A:312 , ILE A:329 , HIS A:340 , GLU A:448 , GOL A:1733 , HOH A:2697
BINDING SITE FOR RESIDUE PGR A1759
29
DC2
SOFTWARE
ALA A:378 , SER A:380 , THR A:389
BINDING SITE FOR RESIDUE PGR A1760
30
DC3
SOFTWARE
TYR A:105 , THR A:262 , LEU A:411 , GLU A:412 , TYR A:413
BINDING SITE FOR RESIDUE PGR A1761
31
DC4
SOFTWARE
ASP A:433 , SER A:440 , ARG A:441 , THR A:442
BINDING SITE FOR RESIDUE PGR A1762
32
DC5
SOFTWARE
THR A:290 , SER A:440 , ARG A:441
BINDING SITE FOR RESIDUE PGR A1763
33
DC6
SOFTWARE
MET A:503 , ASP A:504 , GLN A:506 , ILE A:523 , PGR A:1779 , HOH A:2516 , HOH A:2699
BINDING SITE FOR RESIDUE PGR A1764
34
DC7
SOFTWARE
ARG A:447 , SER A:508 , ILE A:509 , PGR A:1779 , HOH A:2193
BINDING SITE FOR RESIDUE PGR A1765
35
DC8
SOFTWARE
PRO A:568 , SER A:569 , PHE A:594 , LYS A:595 , GOL A:1732 , HOH A:2567
BINDING SITE FOR RESIDUE PGR A1766
36
DC9
SOFTWARE
ARG A:75 , ASN A:653 , ASN A:684 , ASN A:685 , GLU A:686 , HIS A:720 , GOL A:1735
BINDING SITE FOR RESIDUE PGR A1767
37
EC1
SOFTWARE
VAL A:104 , GLU A:415
BINDING SITE FOR RESIDUE PGR A1768
38
EC2
SOFTWARE
ASP A:304 , GLN A:306 , HOH A:2393
BINDING SITE FOR RESIDUE PGR A1769
39
EC3
SOFTWARE
TYR A:103 , SER A:408 , GLN A:409 , HOH A:2146 , HOH A:2159 , HOH A:2433
BINDING SITE FOR RESIDUE PGR A1770
40
EC4
SOFTWARE
ALA A:17 , LYS A:19 , TRP A:50 , HOH A:2700 , HOH A:2701 , HOH A:2702 , HOH A:2703
BINDING SITE FOR RESIDUE PGR A1771
41
EC5
SOFTWARE
ARG A:56 , ILE A:62 , MET A:693 , HOH A:2088 , HOH A:2650
BINDING SITE FOR RESIDUE PGR A1772
42
EC6
SOFTWARE
ARG A:295 , GLU A:319
BINDING SITE FOR RESIDUE PGR A1773
43
EC7
SOFTWARE
ARG A:463 , PHE A:464 , PHE A:559 , HOH A:2704
BINDING SITE FOR RESIDUE PGR A1774
44
EC8
SOFTWARE
ARG A:52 , ASP A:54 , PGR A:1746 , PGR A:1780
BINDING SITE FOR RESIDUE PGR A1775
45
EC9
SOFTWARE
GLY A:333 , GLN A:334 , LYS A:445 , VAL A:446 , GLU A:448 , HOH A:2705
BINDING SITE FOR RESIDUE PGR A1776
46
FC1
SOFTWARE
GLN A:657 , SER A:699 , GLU A:709 , SER A:710 , GLN A:713 , PGO A:1743 , HOH A:2614 , HOH A:2706
BINDING SITE FOR RESIDUE PGR A1777
47
FC2
SOFTWARE
ASP A:32 , GLY A:34 , PRO A:35 , ASN A:249 , TRP A:622 , HOH A:2707
BINDING SITE FOR RESIDUE PGR A1778
48
FC3
SOFTWARE
GLN A:506 , SER A:508 , PGR A:1764 , PGR A:1765 , PO4 A:1793
BINDING SITE FOR RESIDUE PGR A1779
49
FC4
SOFTWARE
ASP A:53 , ASP A:55 , PGR A:1746 , PGR A:1775
BINDING SITE FOR RESIDUE PGR A1780
50
FC5
SOFTWARE
LYS A:284 , GLU A:397 , PHE A:432 , ARG A:441
BINDING SITE FOR RESIDUE PGR A1781
51
FC6
SOFTWARE
GLU A:650 , ASP A:683 , ASN A:684 , ASN A:685 , HOH A:2710
BINDING SITE FOR RESIDUE PGR A1782
52
FC7
SOFTWARE
ASP A:54 , ARG A:56 , GLU A:222 , PRO A:616 , TRP A:668
BINDING SITE FOR RESIDUE PGR A1783
53
FC8
SOFTWARE
LEU A:638 , ASN A:645 , VAL A:646 , ARG A:647 , HOH A:2711 , HOH A:2712
BINDING SITE FOR RESIDUE PGR A1784
54
FC9
SOFTWARE
ASN A:66 , LYS A:69 , GLN A:73
BINDING SITE FOR RESIDUE PGR A1785
55
GC1
SOFTWARE
LEU A:342 , ASP A:344 , ALA A:387
BINDING SITE FOR RESIDUE PGR A1786
56
GC2
SOFTWARE
ASP A:281 , LYS A:284 , HIS A:288 , GLU A:292
BINDING SITE FOR RESIDUE PGR A1787
57
GC3
SOFTWARE
ARG A:283 , LYS A:459 , VAL A:460 , HOH A:2713
BINDING SITE FOR RESIDUE PGR A1788
58
GC4
SOFTWARE
GLU A:246 , HOH A:2714 , HOH A:2715
BINDING SITE FOR RESIDUE PGR A1789
59
GC5
SOFTWARE
ALA A:368 , LEU A:532 , HOH A:2716 , HOH A:2717
BINDING SITE FOR RESIDUE PGR A1790
60
GC6
SOFTWARE
TYR A:496 , ARG A:576 , SER A:577 , HIS A:697 , PHE A:698 , PO4 A:1793 , HOH A:2719 , HOH A:2720 , VAL B:3 , RGL B:4
BINDING SITE FOR RESIDUE PO4 A1791
61
GC7
SOFTWARE
GLY A:201 , LYS A:220 , ASP A:221 , LEU A:224 , HOH A:2250
BINDING SITE FOR RESIDUE PO4 A1792
62
GC8
SOFTWARE
TYR A:494 , TYR A:496 , LEU A:501 , MET A:503 , ARG A:576 , PGR A:1779 , PO4 A:1791
BINDING SITE FOR RESIDUE PO4 A1793
63
GC9
SOFTWARE
TRP A:208 , HOH A:2204 , HOH A:2309
BINDING SITE FOR RESIDUE CL A1794
64
HC1
SOFTWARE
ILE A:91 , ILE A:94 , HOH A:2131 , HOH A:2132 , HOH A:2138
BINDING SITE FOR RESIDUE NA A1795
65
HC2
SOFTWARE
LYS A:121 , HOH A:2173 , HOH A:2194
BINDING SITE FOR RESIDUE CL A1796
66
HC3
SOFTWARE
ASP A:174 , SER A:176 , ASN A:178 , VAL A:180 , HOH A:2216 , HOH A:2226
BINDING SITE FOR RESIDUE NA A1797
67
HC4
SOFTWARE
HIS A:308 , HIS A:312 , PHE A:385
BINDING SITE FOR RESIDUE CL A1798
68
HC5
SOFTWARE
GLU A:63 , ASN A:66 , HOH A:2093 , HOH A:2094
BINDING SITE FOR RESIDUE CL A1799
69
HC6
SOFTWARE
GLU A:226 , SER A:253 , TYR A:496 , TYR A:499 , LEU A:501 , SER A:577 , ALA A:578 , PHE A:603 , MET A:610 , LEU A:617 , GLU A:621 , ARG A:664 , VAL A:665 , HIS A:697 , PO4 A:1791 , HOH A:2266 , HOH A:2267 , HOH A:2302 , HOH A:2303 , HOH A:2580 , HOH A:2622 , HOH A:2678 , HOH A:2679 , HOH A:2680 , HOH A:2681
BINDING SITE FOR CHAIN B OF RESIDUES 1 TO 4
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_2xe4A01 (A:505-724)
2a: PFAM_Peptidase_S9_N_2xe4A02 (A:27-447)
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Clans
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Families
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Organisms
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(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Leishmania major
(1)
1a
Peptidase_S9-2xe4A01
A:505-724
Clan
:
Beta_propeller
(192)
Family
:
Peptidase_S9_N
(11)
Leishmania major
(1)
2a
Peptidase_S9_N-2xe4A02
A:27-447
[
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]
Atom Selection
(currently selected atoms:
all
)
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Miscellaneous
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Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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