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1R64
Asym. Unit
Info
Asym.Unit (180 KB)
Biol.Unit 1 (89 KB)
Biol.Unit 2 (87 KB)
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(1)
Title
:
THE 2.2 A CRYSTAL STRUCTURE OF KEX2 PROTEASE IN COMPLEX WITH AC-ARG-GLU-LYS-BOROARG PEPTIDYL BORONIC ACID INHIBITOR
Authors
:
T. Holyoak, C. A. Kettner, G. A. Petsko, R. S. Fuller, D. Ringe
Date
:
14 Oct 03 (Deposition) - 09 Mar 04 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Kex2, Kexin, Protease, Protein Convertase, Prohormone Processing, Proprotein Convertase, Subtilisin, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Holyoak, C. A. Kettner, G. A. Petsko, R. S. Fuller, D. Ringe
Structural Basis For Differences In Substrate Selectivity I Kex2 And Furin Protein Convertases
Biochemistry V. 43 2412 2004
[
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Hetero Components
(6, 24)
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: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-... (BTBa)
4a: CALCIUM ION (CAa)
4b: CALCIUM ION (CAb)
4c: CALCIUM ION (CAc)
4d: CALCIUM ION (CAd)
4e: CALCIUM ION (CAe)
4f: CALCIUM ION (CAf)
5a: POTASSIUM ION (Ka)
5b: POTASSIUM ION (Kb)
5c: POTASSIUM ION (Kc)
5d: POTASSIUM ION (Kd)
5e: POTASSIUM ION (Ke)
5f: POTASSIUM ION (Kf)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
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
BTB
1
Ligand/Ion
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4
CA
6
Ligand/Ion
CALCIUM ION
5
K
6
Ligand/Ion
POTASSIUM ION
6
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:163 , ILE A:164 , GLU A:400
BINDING SITE FOR RESIDUE NAG A 903
02
AC2
SOFTWARE
ALA A:401 , ASN A:402 , ASN A:404 , SER A:456 , LYS A:457 , ASN A:461 , HOH A:984 , HOH A:1108 , HOH A:1148
BINDING SITE FOR RESIDUE NAG A 906
03
AC3
SOFTWARE
ASN B:163 , ILE B:164 , GLU B:400
BINDING SITE FOR RESIDUE NAG B 903
04
AC4
SOFTWARE
ASP A:277 , ASP A:320 , GLU A:350 , HOH A:1128 , HOH A:1129 , HOH A:1130
BINDING SITE FOR RESIDUE CA A 700
05
AC5
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 701
06
AC6
SOFTWARE
THR A:328 , SER A:330 , SER A:333 , THR A:335 , HOH A:959
BINDING SITE FOR RESIDUE CA A 702
07
AC7
SOFTWARE
ALA A:191 , GLU A:192 , SER A:194 , TYR A:261
BINDING SITE FOR RESIDUE K A 800
08
AC8
SOFTWARE
THR A:466 , TRP A:467 , ALA A:500 , HOH A:1221
BINDING SITE FOR RESIDUE K A 801
09
AC9
SOFTWARE
LEU A:246 , HOH A:1244 , HOH B:1920 , HOH B:2002 , HOH B:2043 , HOH C:988
BINDING SITE FOR RESIDUE K A 802
10
BC1
SOFTWARE
ASP B:277 , ASP B:320 , GLU B:350 , HOH B:1950 , HOH B:2003 , HOH B:2029
BINDING SITE FOR RESIDUE CA B 700
11
BC2
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 701
12
BC3
SOFTWARE
THR B:328 , SER B:330 , SER B:333 , THR B:335 , HOH B:1911
BINDING SITE FOR RESIDUE CA B 702
13
BC4
SOFTWARE
ALA B:191 , GLU B:192 , SER B:194 , TYR B:261
BINDING SITE FOR RESIDUE K B 800
14
BC5
SOFTWARE
THR B:466 , TRP B:467 , ALA B:500 , HOH B:2172 , HOH B:2175 , HOH B:2176
BINDING SITE FOR RESIDUE K B 801
15
BC6
SOFTWARE
HOH B:2083
BINDING SITE FOR RESIDUE K B 803
16
BC7
SOFTWARE
ARG A:318 , HOH A:1135 , ASP B:431 , SER B:432 , ALA B:433 , ALA B:530 , ILE B:532 , HOH B:1956 , HOH B:1957 , HOH B:2005 , HOH B:2035 , LYS C:4 , HOH C:281 , HOH C:306
BINDING SITE FOR RESIDUE BTB B1901
17
BC8
SOFTWARE
ASN A:480 , ASN A:577 , GLY A:578 , ARG A:580 , HOH A:1269
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 480 RESIDUES 904 TO 905
18
BC9
SOFTWARE
ASN B:480 , GLY B:578 , ARG B:580 , HOH B:2184
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 480 RESIDUES 904 TO 905
19
CC1
SOFTWARE
ASP A:176 , ASP A:210 , HIS A:213 , LEU A:246 , ILE A:250 , GLU A:255 , SER A:272 , TRP A:273 , GLY A:274 , PRO A:275 , ASP A:277 , GLN A:283 , ALA A:311 , GLY A:313 , ASN A:314 , ASP A:325 , THR A:328 , THR A:384 , SER A:385 , HOH A:971 , HOH A:993 , HOH A:1128 , HOH A:1271 , BTB B:1901 , HOH B:2043 , HOH C:135 , HOH C:156 , HOH C:281 , HOH C:306 , HOH C:320 , HOH C:343 , HOH C:465 , HOH C:988
BINDING SITE FOR CHAIN C OF AC-ARG-GLU-LYS- BOROARG PEPTIDE INHIBITOR
20
CC2
SOFTWARE
HOH A:1294 , ASP B:176 , ASP B:210 , HIS B:213 , LEU B:246 , ILE B:250 , GLU B:255 , SER B:272 , TRP B:273 , GLY B:274 , PRO B:275 , ASP B:277 , GLN B:283 , ALA B:311 , GLY B:313 , ASN B:314 , ASP B:325 , THR B:328 , GLY B:382 , GLY B:383 , THR B:384 , SER B:385 , HOH B:1945 , HOH B:2029 , HOH B:2126 , HOH B:2154 , HOH D:398 , HOH D:941
BINDING SITE FOR CHAIN D OF AC-ARG-GLU-LYS- BOROARG 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)
;
View:
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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:121-601 | B:121-601)
View:
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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:121-601
B:121-601
481
481
[
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]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1r64a1 (A:461-601)
1b: SCOP_d1r64b1 (B:461-601)
2a: SCOP_d1r64a2 (A:121-460)
2b: SCOP_d1r64b2 (B:121-460)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d1r64a1
A:461-601
1b
d1r64b1
B:461-601
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
d1r64a2
A:121-460
2b
d1r64b2
B:121-460
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1r64A01 (A:123-461)
1b: CATH_1r64B01 (B:123-461)
2a: CATH_1r64A02 (A:462-599)
2b: CATH_1r64B02 (B:462-599)
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Organisms
(
)
(
)
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
1r64A01
A:123-461
1b
1r64B01
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
1r64A02
A:462-599
2b
1r64B02
B:462-599
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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