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3ZUK
Asym. Unit
Info
Asym.Unit (445 KB)
Biol.Unit 1 (221 KB)
Biol.Unit 2 (220 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE ZMP1 IN COMPLEX WITH INHIBITOR
Authors
:
D. M. Ferraris, D. Sbardella, A. Petrera, S. Marini, B. Amstutz, M. Cole P. Sander, M. Rizzi
Date
:
19 Jul 11 (Deposition) - 03 Aug 11 (Release) - 21 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydrolase-Inhibitor Complex, Pathogenicity, Phagosome Maturation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Ferraris, D. Sbardella, A. Petrera, S. Marini, B. Amstutz, M. Coletta, P. Sander, M. Rizzi
Crystal Structure Of Mycobacterium Tuberculosis Zinc-Dependent Metalloprotease-1 (Zmp1), A Metalloprotease Involved In Pathogenicity.
J. Biol. Chem. V. 286 32475 2011
[
close entry info
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Hetero Components
(10, 70)
Info
All Hetero Components
01a: 2,2',2''-NITRILOTRIETHANOL (211a)
02a: ACETATE ION (ACTa)
02b: ACETATE ION (ACTb)
02c: ACETATE ION (ACTc)
02d: ACETATE ION (ACTd)
02e: ACETATE ION (ACTe)
02f: ACETATE ION (ACTf)
02g: ACETATE ION (ACTg)
02h: ACETATE ION (ACTh)
02i: ACETATE ION (ACTi)
02j: ACETATE ION (ACTj)
02k: ACETATE ION (ACTk)
02l: ACETATE ION (ACTl)
02m: ACETATE ION (ACTm)
03a: CALCIUM ION (CAa)
04a: CHLORIDE ION (CLa)
04b: CHLORIDE ION (CLb)
04c: CHLORIDE ION (CLc)
05a: DI(HYDROXYETHYL)ETHER (PEGa)
05aa: DI(HYDROXYETHYL)ETHER (PEGaa)
05ab: DI(HYDROXYETHYL)ETHER (PEGab)
05ac: DI(HYDROXYETHYL)ETHER (PEGac)
05ad: DI(HYDROXYETHYL)ETHER (PEGad)
05b: DI(HYDROXYETHYL)ETHER (PEGb)
05c: DI(HYDROXYETHYL)ETHER (PEGc)
05d: DI(HYDROXYETHYL)ETHER (PEGd)
05e: DI(HYDROXYETHYL)ETHER (PEGe)
05f: DI(HYDROXYETHYL)ETHER (PEGf)
05g: DI(HYDROXYETHYL)ETHER (PEGg)
05h: DI(HYDROXYETHYL)ETHER (PEGh)
05i: DI(HYDROXYETHYL)ETHER (PEGi)
05j: DI(HYDROXYETHYL)ETHER (PEGj)
05k: DI(HYDROXYETHYL)ETHER (PEGk)
05l: DI(HYDROXYETHYL)ETHER (PEGl)
05m: DI(HYDROXYETHYL)ETHER (PEGm)
05n: DI(HYDROXYETHYL)ETHER (PEGn)
05o: DI(HYDROXYETHYL)ETHER (PEGo)
05p: DI(HYDROXYETHYL)ETHER (PEGp)
05q: DI(HYDROXYETHYL)ETHER (PEGq)
05r: DI(HYDROXYETHYL)ETHER (PEGr)
05s: DI(HYDROXYETHYL)ETHER (PEGs)
05t: DI(HYDROXYETHYL)ETHER (PEGt)
05u: DI(HYDROXYETHYL)ETHER (PEGu)
05v: DI(HYDROXYETHYL)ETHER (PEGv)
05w: DI(HYDROXYETHYL)ETHER (PEGw)
05x: DI(HYDROXYETHYL)ETHER (PEGx)
05y: DI(HYDROXYETHYL)ETHER (PEGy)
05z: DI(HYDROXYETHYL)ETHER (PEGz)
06a: TETRAETHYLENE GLYCOL (PG4a)
06b: TETRAETHYLENE GLYCOL (PG4b)
06c: TETRAETHYLENE GLYCOL (PG4c)
06d: TETRAETHYLENE GLYCOL (PG4d)
07a: TRIETHYLENE GLYCOL (PGEa)
07b: TRIETHYLENE GLYCOL (PGEb)
07c: TRIETHYLENE GLYCOL (PGEc)
07d: TRIETHYLENE GLYCOL (PGEd)
07e: TRIETHYLENE GLYCOL (PGEe)
07f: TRIETHYLENE GLYCOL (PGEf)
07g: TRIETHYLENE GLYCOL (PGEg)
07h: TRIETHYLENE GLYCOL (PGEh)
08a: N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDRO... (RDFa)
08b: N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDRO... (RDFb)
09a: SULFATE ION (SO4a)
09b: SULFATE ION (SO4b)
09c: SULFATE ION (SO4c)
09d: SULFATE ION (SO4d)
09e: SULFATE ION (SO4e)
09f: SULFATE ION (SO4f)
10a: ZINC ION (ZNa)
10b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
211
1
Ligand/Ion
2,2',2''-NITRILOTRIETHANOL
2
ACT
13
Ligand/Ion
ACETATE ION
3
CA
1
Ligand/Ion
CALCIUM ION
4
CL
3
Ligand/Ion
CHLORIDE ION
5
PEG
30
Ligand/Ion
DI(HYDROXYETHYL)ETHER
6
PG4
4
Ligand/Ion
TETRAETHYLENE GLYCOL
7
PGE
8
Ligand/Ion
TRIETHYLENE GLYCOL
8
RDF
2
Ligand/Ion
N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
9
SO4
6
Ligand/Ion
SULFATE ION
10
ZN
2
Ligand/Ion
ZINC ION
[
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
HIS A:493 , HIS A:497 , GLU A:560 , RDF A:1665
BINDING SITE FOR RESIDUE ZN A1664
02
AC2
SOFTWARE
HIS B:493 , HIS B:497 , GLU B:560 , RDF B:1665
BINDING SITE FOR RESIDUE ZN B1664
03
AC3
SOFTWARE
PHE B:48 , ASN B:452 , ALA B:453 , TYR B:454 , ILE B:468 , HIS B:493 , GLU B:494 , HIS B:497 , GLU B:560 , HIS B:622 , ARG B:628 , ZN B:1664 , ACT B:1691 , HOH B:2071 , HOH B:2171
BINDING SITE FOR RESIDUE RDF B1665
04
AC4
SOFTWARE
PHE A:48 , VAL A:451 , ASN A:452 , ALA A:453 , TYR A:454 , HIS A:493 , GLU A:494 , HIS A:497 , GLU A:560 , ARG A:616 , HIS A:622 , ARG A:628 , ZN A:1664 , 211 A:1666 , PGE A:1684 , ACT A:1689 , HOH A:2148
BINDING SITE FOR RESIDUE RDF A1665
05
AC5
SOFTWARE
ARG A:615 , ARG A:616 , ASP A:620 , RDF A:1665
BINDING SITE FOR RESIDUE 211 A1666
06
AC6
SOFTWARE
ARG B:126 , THR B:248 , ALA B:249
BINDING SITE FOR RESIDUE PEG B1666
07
AC7
SOFTWARE
PRO A:6 , SER A:7 , GLY A:8 , ASP A:10
BINDING SITE FOR RESIDUE PEG A1667
08
AC8
SOFTWARE
GLN B:153 , SER B:154 , GLY B:155 , ILE B:156 , ARG B:219 , HOH B:2051
BINDING SITE FOR RESIDUE PEG B1667
09
AC9
SOFTWARE
PHE A:52 , VAL A:329 , GLU A:333 , GLN A:449
BINDING SITE FOR RESIDUE PEG A1668
10
BC1
SOFTWARE
SER B:162 , ASP B:166 , HIS B:169 , ILE B:614 , LEU B:617 , ALA B:618 , HOH B:2140
BINDING SITE FOR RESIDUE PEG B1668
11
BC2
SOFTWARE
SER A:86 , PRO A:100 , TRP A:298 , ASP A:414 , ASP A:415 , LEU A:416 , TYR A:417
BINDING SITE FOR RESIDUE PEG A1669
12
BC3
SOFTWARE
ALA A:77 , HOH A:2019
BINDING SITE FOR RESIDUE PEG A1670
13
BC4
SOFTWARE
ASN A:227 , LEU A:228 , ARG A:229
BINDING SITE FOR RESIDUE PEG A1671
14
BC5
SOFTWARE
GLN A:641 , ASP A:644 , VAL A:645 , PGE A:1683 , GLN B:576 , LEU B:577 , ASN B:580 , GLY B:581
BINDING SITE FOR RESIDUE PEG A1672
15
BC6
SOFTWARE
GLN B:576 , ALA B:638
BINDING SITE FOR RESIDUE PEG B1669
16
BC7
SOFTWARE
GLN A:534 , ARG A:634 , ARG A:657 , PEG A:1679 , ASP B:545 , PRO B:547 , GLY B:548
BINDING SITE FOR RESIDUE PEG B1670
17
BC8
SOFTWARE
THR B:123 , ARG B:126 , ALA B:127 , ALA B:425
BINDING SITE FOR RESIDUE PEG B1671
18
BC9
SOFTWARE
ASP B:15
BINDING SITE FOR RESIDUE PEG B1672
19
CC1
SOFTWARE
ASP A:479 , GLU A:480 , HOH A:2117 , HOH A:2139 , ILE B:5 , ASP B:479
BINDING SITE FOR RESIDUE PEG A1673
20
CC2
SOFTWARE
ASP B:138 , THR B:139 , SER B:141 , ASN B:456 , PRO B:457 , GLY B:458 , TYR B:506
BINDING SITE FOR RESIDUE PEG B1673
21
CC3
SOFTWARE
ARG A:126
BINDING SITE FOR RESIDUE PEG A1674
22
CC4
SOFTWARE
LYS B:354 , ASP B:358 , ALA B:395 , LYS B:396 , VAL B:397 , TYR B:399 , ILE B:401 , TRP B:444
BINDING SITE FOR RESIDUE PEG B1674
23
CC5
SOFTWARE
THR A:152 , ARG A:219 , ARG A:263
BINDING SITE FOR RESIDUE PEG A1675
24
CC6
SOFTWARE
ALA A:613 , ARG A:616 , LEU A:617 , ASP A:620 , HIS A:622 , SER A:623 , PRO A:624 , PRO A:625 , HOH A:2147
BINDING SITE FOR RESIDUE PEG A1676
25
CC7
SOFTWARE
ASP A:358 , ASP A:362 , ALA A:395
BINDING SITE FOR RESIDUE PEG A1677
26
CC8
SOFTWARE
ASP A:17 , ALA A:18 , ARG A:19 , ASP A:22 , ASP A:23 , PEG A:1680 , ACT A:1688
BINDING SITE FOR RESIDUE PEG A1678
27
CC9
SOFTWARE
ASN A:582 , ALA B:4 , SER B:7 , ASP B:588
BINDING SITE FOR RESIDUE PEG B1675
28
DC1
SOFTWARE
VAL A:544 , ASP A:545 , ASP B:22 , ARG B:541 , GLU B:626 , PHE B:627 , ASN B:630 , LEU B:651
BINDING SITE FOR RESIDUE PEG B1676
29
DC2
SOFTWARE
GLU A:533 , GLN A:534 , ARG A:657 , PEG B:1670
BINDING SITE FOR RESIDUE PEG A1679
30
DC3
SOFTWARE
VAL B:216 , ARG B:220 , ACT B:1694 , SO4 B:1697
BINDING SITE FOR RESIDUE PEG B1677
31
DC4
SOFTWARE
LYS B:392 , ASP B:507 , GLY B:508 , VAL B:513 , HOH B:2105
BINDING SITE FOR RESIDUE PEG B1678
32
DC5
SOFTWARE
ASP A:22 , PEG A:1678 , ASP B:545
BINDING SITE FOR RESIDUE PEG A1680
33
DC6
SOFTWARE
GLU A:116 , ASN B:227 , ARG B:229
BINDING SITE FOR RESIDUE PEG B1679
34
DC7
SOFTWARE
ASN A:363 , ALA A:574 , LEU A:577 , ASN A:580
BINDING SITE FOR RESIDUE PEG A1681
35
DC8
SOFTWARE
PHE B:349 , ALA B:353 , LYS B:354
BINDING SITE FOR RESIDUE PEG B1680
36
DC9
SOFTWARE
ASN A:580 , HIS B:27 , GLY B:589 , GLN B:594 , PG4 B:1685
BINDING SITE FOR RESIDUE PGE B1681
37
EC1
SOFTWARE
GLU A:374 , LEU A:573 , ASP B:637 , ARG B:658 , HOH B:2161 , HOH B:2163
BINDING SITE FOR RESIDUE PGE A1682
38
EC2
SOFTWARE
ASP B:221 , ASP B:501 , LYS B:505 , ASP B:514 , TRP B:516
BINDING SITE FOR RESIDUE PGE B1682
39
EC3
SOFTWARE
ASP A:637 , GLN A:641 , ARG A:658 , PEG A:1672
BINDING SITE FOR RESIDUE PGE A1683
40
EC4
SOFTWARE
TYR A:454 , TYR A:455 , HIS A:497 , RDF A:1665
BINDING SITE FOR RESIDUE PGE A1684
41
EC5
SOFTWARE
LEU A:579 , ALA A:584 , HOH A:2144 , LEU B:579 , ALA B:584 , ACT B:1687 , HOH B:2150
BINDING SITE FOR RESIDUE PGE B1683
42
EC6
SOFTWARE
GLN A:319 , LYS A:607 , ARG A:609 , ASP B:648
BINDING SITE FOR RESIDUE PGE A1685
43
EC7
SOFTWARE
ALA A:16 , HIS A:27 , ASP A:588 , GLY A:589 , GLN A:594 , HOH A:2006
BINDING SITE FOR RESIDUE PGE A1686
44
EC8
SOFTWARE
PRO B:540 , ASP B:542 , GLN B:553 , THR B:557 , ALA B:613 , ARG B:616 , LEU B:617 , ASP B:620 , HIS B:622 , PRO B:624 , GLU B:626 , HOH B:2153
BINDING SITE FOR RESIDUE PG4 B1684
45
EC9
SOFTWARE
HIS A:13 , TRP A:32 , GLU A:35 , HIS A:36 , ASP A:45 , SER A:50
BINDING SITE FOR RESIDUE PG4 A1687
46
FC1
SOFTWARE
LEU B:11 , ALA B:16 , ARG B:19 , HIS B:27 , PGE B:1681 , HOH B:2010 , HOH B:2149
BINDING SITE FOR RESIDUE PG4 B1685
47
FC2
SOFTWARE
VAL A:544 , ASP A:545 , HIS A:546 , HOH A:2133 , GLN B:534 , TYR B:538 , ARG B:634 , ARG B:657
BINDING SITE FOR RESIDUE PG4 B1686
48
FC3
SOFTWARE
GLY A:581 , THR B:591 , MET B:593 , PGE B:1683 , HOH B:2150 , HOH B:2173
BINDING SITE FOR RESIDUE ACT B1687
49
FC4
SOFTWARE
ASP A:15 , GLY A:30 , ARG A:541 , PEG A:1678
BINDING SITE FOR RESIDUE ACT A1688
50
FC5
SOFTWARE
TYR B:147 , ALA B:256 , MET B:257 , THR B:258
BINDING SITE FOR RESIDUE ACT B1688
51
FC6
SOFTWARE
PHE A:445 , RDF A:1665
BINDING SITE FOR RESIDUE ACT A1689
52
FC7
SOFTWARE
ASP B:15 , GLY B:30
BINDING SITE FOR RESIDUE ACT B1689
53
FC8
SOFTWARE
ASP B:10
BINDING SITE FOR RESIDUE ACT B1690
54
FC9
SOFTWARE
TYR B:455 , HIS B:497 , RDF B:1665 , ACT B:1694
BINDING SITE FOR RESIDUE ACT B1691
55
GC1
SOFTWARE
GLN B:125 , GLY B:134 , VAL B:135
BINDING SITE FOR RESIDUE ACT B1692
56
GC2
SOFTWARE
ACT A:1691 , ASP B:479 , TYR B:575 , LEU B:579 , PRO B:585
BINDING SITE FOR RESIDUE ACT B1693
57
GC3
SOFTWARE
TRP A:516 , ARG A:521
BINDING SITE FOR RESIDUE ACT A1690
58
GC4
SOFTWARE
ILE A:5 , ASN B:582 , ACT B:1693
BINDING SITE FOR RESIDUE ACT A1691
59
GC5
SOFTWARE
HIS B:497 , PEG B:1677 , ACT B:1691 , HOH B:2073
BINDING SITE FOR RESIDUE ACT B1694
60
GC6
SOFTWARE
GLN A:125 , VAL A:129 , VAL A:135
BINDING SITE FOR RESIDUE ACT A1692
61
GC7
SOFTWARE
LEU A:577 , ASN A:580 , ASP B:644 , VAL B:645 , HOH B:2163
BINDING SITE FOR RESIDUE SO4 B1695
62
GC8
SOFTWARE
HIS A:536 , HIS A:551 , VAL A:552 , GLN A:553 , GLY A:554 , ALA A:555 , HOH A:2159
BINDING SITE FOR RESIDUE SO4 A1693
63
GC9
SOFTWARE
ILE B:532 , HIS B:536 , GLN B:553 , GLY B:554 , ALA B:555
BINDING SITE FOR RESIDUE SO4 B1696
64
HC1
SOFTWARE
THR B:152 , ARG B:219 , ARG B:263 , PEG B:1677 , HOH B:2045
BINDING SITE FOR RESIDUE SO4 B1697
65
HC2
SOFTWARE
ARG A:42 , ALA A:43 , ARG A:49 , HOH A:2086
BINDING SITE FOR RESIDUE SO4 A1694
66
HC3
SOFTWARE
ARG B:42 , ALA B:43 , THR B:44 , ARG B:49
BINDING SITE FOR RESIDUE SO4 B1698
67
HC4
SOFTWARE
ASP B:242 , ILE B:411
BINDING SITE FOR RESIDUE CL B1699
68
HC5
SOFTWARE
TYR A:147 , LEU A:435
BINDING SITE FOR RESIDUE CL A1695
69
HC6
SOFTWARE
ASP B:113 , GLU B:116 , ASP B:412 , ASP B:414
BINDING SITE FOR RESIDUE CA B1700
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3zuka_ (A:)
1b: SCOP_d3zukb_ (B:)
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
automated matches
(37)
Protein domain
:
automated matches
(37)
Mycobacterium tuberculosis [TaxId: 83332]
(1)
1a
d3zuka_
A:
1b
d3zukb_
B:
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CATH Domains
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all CATH domains
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Asym.Unit (445 KB)
Header - Asym.Unit
Biol.Unit 1 (221 KB)
Header - Biol.Unit 1
Biol.Unit 2 (220 KB)
Header - Biol.Unit 2
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