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1OT5
Asym. Unit
Info
Asym.Unit (171 KB)
Biol.Unit 1 (84 KB)
Biol.Unit 2 (84 KB)
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(1)
Title
:
THE 2.4 ANGSTROM CRYSTAL STRUCTURE OF KEX2 IN COMPLEX WITH A PEPTIDYL-BORONIC ACID INHIBITOR
Authors
:
T. Holyoak, M. A. Wilson, T. D. Fenn, C. A. Kettner, G. A. Petsko, R. S. Ful D. Ringe
Date
:
21 Mar 03 (Deposition) - 17 Jun 03 (Release) - 14 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Subtilisin Fold, Peptidyl-Boronic Acid, Serine Protease, P-Domain, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
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Reference
:
T. Holyoak, M. A. Wilson, T. D. Fenn, C. A. Kettner, G. A. Petsko, R. S. Fuller, D. Ringe
2. 4 A Resolution Crystal Structure Of The Prototypical Hormone-Processing Protease Kex2 In Complex With An Ala-Lys-Arg Boronic Acid Inhibitor
Biochemistry V. 42 6709 2003
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: (1R)-1-AMINO-4-{[(E)-AMINO(IMINO)M... (BORa)
2b: (1R)-1-AMINO-4-{[(E)-AMINO(IMINO)M... (BORb)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
2
Mod. Amino Acid
ACETYL GROUP
2
BOR
2
Mod. Amino Acid
(1R)-1-AMINO-4-{[(E)-AMINO(IMINO)METHYL]AMINO}BUTYLBORONIC ACID
3
CA
6
Ligand/Ion
CALCIUM ION
4
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:163 , ALA A:167 , GLU A:400 , HOH A:648
BINDING SITE FOR RESIDUE NAG A 603
02
AC2
SOFTWARE
ASN B:163 , ALA B:167 , GLU B:400 , HOH B:726
BINDING SITE FOR RESIDUE NAG B 603
03
AC3
SOFTWARE
ASP A:277 , ASP A:320 , GLU A:350 , HOH A:607 , HOH A:618 , HOH A:623
BINDING SITE FOR RESIDUE CA A 600
04
AC4
SOFTWARE
ASP A:135 , ASP A:184 , LYS A:224 , ASN A:227 , PHE A:229 , GLY A:231
BINDING SITE FOR RESIDUE CA A 601
05
AC5
SOFTWARE
THR A:328 , SER A:330 , SER A:333 , THR A:335 , HOH A:609
BINDING SITE FOR RESIDUE CA A 602
06
AC6
SOFTWARE
ASP B:277 , ASP B:320 , GLU B:350 , HOH B:610 , HOH B:615 , HOH B:633
BINDING SITE FOR RESIDUE CA B 600
07
AC7
SOFTWARE
ASP B:135 , ASP B:184 , LYS B:224 , ASN B:227 , PHE B:229 , GLY B:231
BINDING SITE FOR RESIDUE CA B 601
08
AC8
SOFTWARE
THR B:328 , SER B:330 , SER B:333 , THR B:335 , HOH B:606
BINDING SITE FOR RESIDUE CA B 602
09
AC9
SOFTWARE
ASN A:480 , GLY A:578 , ARG A:580 , HOH A:759 , HOH A:770
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 480 RESIDUES 604 TO 605
10
BC1
SOFTWARE
ASN B:480 , GLY B:578 , ARG B:580 , HOH B:817
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 480 RESIDUES 604 TO 605
11
BC2
SOFTWARE
ASP A:176 , ASP A:210 , HIS A:213 , SER A:272 , TRP A:273 , GLY A:274 , PRO A:275 , ASP A:277 , ALA A:311 , ASN A:314 , ASP A:325 , THR A:328 , GLY A:382 , GLY A:383 , SER A:385 , HOH A:729 , HOH A:738 , HOH C:89 , HOH C:315 , HOH C:426
BINDING SITE FOR CHAIN C OF AC-ALA-LYS-BOROARG N -ACETYLATED BORONIC ACID PEPTIDE INHIBITOR
12
BC3
SOFTWARE
TYR A:474 , ASP B:176 , ASP B:210 , HIS B:213 , SER B:272 , TRP B:273 , GLY B:274 , PRO B:275 , ASP B:277 , ALA B:311 , GLY B:313 , ASN B:314 , ASP B:325 , THR B:328 , SER B:385 , HOH B:814 , HOH D:137 , HOH D:196 , HOH D:248
BINDING SITE FOR CHAIN D OF AC-ALA-LYS-BOROARG N -ACETYLATED BORONIC ACID PEPTIDE INHIBITOR
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: SUBTILASE_ASP (A:171-182,B:171-182)
2: SUBTILASE_HIS (A:213-223,B:213-223)
3: SUBTILASE_SER (A:383-393,B:383-393)
4: P_HOMO_B (A:462-596,B:462-596)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUBTILASE_ASP
PS00136
Serine proteases, subtilase family, aspartic acid active site.
KEX2_YEAST
171-182
2
A:171-182
B:171-182
2
SUBTILASE_HIS
PS00137
Serine proteases, subtilase family, histidine active site.
KEX2_YEAST
213-223
2
A:213-223
B:213-223
3
SUBTILASE_SER
PS00138
Serine proteases, subtilase family, serine active site.
KEX2_YEAST
383-393
2
A:383-393
B:383-393
4
P_HOMO_B
PS51829
P/Homo B domain profile.
KEX2_YEAST
462-596
2
A:462-596
B:462-596
[
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Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:123-599 | B:123-599)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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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
YNL238W
1
YNL238W.1
XIV:202429-204873
2445
KEX2_YEAST
1-814
814
2
A:123-599
B:123-599
477
477
[
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1ot5a1 (A:461-599)
1b: SCOP_d1ot5b1 (B:461-599)
2a: SCOP_d1ot5a2 (A:123-460)
2b: SCOP_d1ot5b2 (B:123-460)
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Protein Domains
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Organisms
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Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
Proprotein convertase P-domain
(7)
Protein domain
:
Kexin, C-terminal domain
(3)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
1a
d1ot5a1
A:461-599
1b
d1ot5b1
B:461-599
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Subtilisin-like
(227)
Superfamily
:
Subtilisin-like
(227)
Family
:
Subtilases
(190)
Protein domain
:
Kexin, N-terminal domain
(3)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
2a
d1ot5a2
A:123-460
2b
d1ot5b2
B:123-460
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1ot5A01 (A:123-461)
1b: CATH_1ot5B01 (B:123-461)
2a: CATH_1ot5A02 (A:462-599)
2b: CATH_1ot5B02 (B:462-599)
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Organisms
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(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.200, no name defined]
(198)
Baker's yeast (Saccharomyces cerevisiae)
(3)
1a
1ot5A01
A:123-461
1b
1ot5B01
B:123-461
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Galactose-binding domain-like
(195)
Baker's yeast (Saccharomyces cerevisiae)
(6)
2a
1ot5A02
A:462-599
2b
1ot5B02
B:462-599
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_P_proprotein_1ot5B01 (B:505-590)
1b: PFAM_P_proprotein_1ot5B02 (B:505-590)
2a: PFAM_Peptidase_S8_1ot5B03 (B:170-454)
2b: PFAM_Peptidase_S8_1ot5B04 (B:170-454)
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Organisms
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Clan
:
GBD
(153)
Family
:
P_proprotein
(2)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
1a
P_proprotein-1ot5B01
B:505-590
1b
P_proprotein-1ot5B02
B:505-590
Clan
:
no clan defined [family: Peptidase_S8]
(104)
Family
:
Peptidase_S8
(104)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
2a
Peptidase_S8-1ot5B03
B:170-454
2b
Peptidase_S8-1ot5B04
B:170-454
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