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2HRQ
Biol. Unit 1
Info
Asym.Unit (539 KB)
Biol.Unit 1 (269 KB)
Biol.Unit 2 (270 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN LIVER CARBOXYLESTERASE 1 (HCE1) IN COVALENT COMPLEX WITH THE NERVE AGENT SOMAN (GD)
Authors
:
C. D. Fleming, M. R. Redinbo
Date
:
20 Jul 06 (Deposition) - 01 May 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Hydrolase, Carboxylesterase, Soman
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. D. Fleming, C. C. Edwards, S. D. Kirby, D. M. Maxwell, P. M. Potter, D. M. Cerasoli, M. R. Redinbo
Crystal Structures Of Human Carboxylesterase 1 In Covalent Complexes With The Chemical Warfare Agents Soman And Tabun.
Biochemistry V. 46 5063 2007
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Hetero Components
(5, 18)
Info
All Hetero Components
1a: (1R)-1,2,2-TRIMETHYLPROPYL (R)-MET... (GD7a)
1b: (1R)-1,2,2-TRIMETHYLPROPYL (R)-MET... (GD7b)
1c: (1R)-1,2,2-TRIMETHYLPROPYL (R)-MET... (GD7c)
1d: (1R)-1,2,2-TRIMETHYLPROPYL (R)-MET... (GD7d)
1e: (1R)-1,2,2-TRIMETHYLPROPYL (R)-MET... (GD7e)
1f: (1R)-1,2,2-TRIMETHYLPROPYL (R)-MET... (GD7f)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3a: O-SIALIC ACID (SIAa)
3b: O-SIALIC ACID (SIAb)
3c: O-SIALIC ACID (SIAc)
3d: O-SIALIC ACID (SIAd)
3e: O-SIALIC ACID (SIAe)
3f: O-SIALIC ACID (SIAf)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
5a: SUCROSE (SUCa)
5b: SUCROSE (SUCb)
5c: SUCROSE (SUCc)
5d: SUCROSE (SUCd)
5e: SUCROSE (SUCe)
5f: SUCROSE (SUCf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GD7
3
Ligand/Ion
(1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE
2
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SIA
3
Ligand/Ion
O-SIALIC ACID
4
SO4
6
Ligand/Ion
SULFATE ION
5
SUC
3
Ligand/Ion
SUCROSE
[
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Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC6 (SOFTWARE)
10: CC1 (SOFTWARE)
11: CC2 (SOFTWARE)
12: CC3 (SOFTWARE)
13: CC4 (SOFTWARE)
14: CC5 (SOFTWARE)
15: CC6 (SOFTWARE)
16: DC4 (SOFTWARE)
17: DC5 (SOFTWARE)
18: DC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:1079 , HOH A:8049 , HOH A:8456 , HOH A:8924 , HOH A:9081
BINDING SITE FOR RESIDUE NAG A 179
02
AC2
SOFTWARE
LEU A:1051 , GLY A:1052 , LYS A:1078 , ASN A:1079 , SER A:1082 , TYR A:1118 , HOH A:8253 , HOH A:8456 , HOH A:8879 , HOH A:9098 , LYS B:2262
BINDING SITE FOR RESIDUE SIA A 182
03
AC3
SOFTWARE
SIA B:282 , ASN B:2079 , ASP C:3260
BINDING SITE FOR RESIDUE NAG B 279
04
AC4
SOFTWARE
NAG B:279 , GLY B:2052 , LYS B:2078 , ASN B:2079 , SER B:2082 , PRO B:2084 , HOH B:8086 , HOH B:8156 , LYS C:3262
BINDING SITE FOR RESIDUE SIA B 282
05
AC5
SOFTWARE
ASP A:1260 , SIA C:382 , ASN C:3079 , HOH C:8315
BINDING SITE FOR RESIDUE NAG C 379
06
AC6
SOFTWARE
LYS A:1262 , NAG C:379 , GLY C:3052 , ASN C:3079 , SER C:3082 , HOH C:8364 , HOH C:8444 , HOH C:8473 , HOH C:8702
BINDING SITE FOR RESIDUE SIA C 382
07
BC4
SOFTWARE
GLY A:1356 , TRP A:1357 , LEU A:1368 , SER A:1369 , GLY A:1371 , LYS A:1414 , LEU A:1418 , MET A:1459 , HOH A:8465
BINDING SITE FOR RESIDUE SUC A 11
08
BC5
SOFTWARE
GLY B:2356 , TRP B:2357 , LEU B:2368 , SER B:2369 , LYS B:2414 , LEU B:2418 , HOH B:8288 , HOH B:8586
BINDING SITE FOR RESIDUE SUC B 22
09
BC6
SOFTWARE
GLY C:3356 , TRP C:3357 , LEU C:3368 , SER C:3369 , GLY C:3371 , LYS C:3414 , LEU C:3418 , HOH C:8115 , HOH C:8331 , HOH C:8396 , HOH C:8445
BINDING SITE FOR RESIDUE SUC C 33
10
CC1
SOFTWARE
LYS A:1130 , HIS A:1284 , GLN A:1288 , HOH A:8521 , GLU C:3114 , LYS C:3289 , THR C:3290 , GLU C:3291 , GLU C:3292 , HOH C:8213
BINDING SITE FOR RESIDUE SO4 C 184
11
CC2
SOFTWARE
HIS A:1284 , ARG A:1287 , HOH A:8154 , LEU C:3060
BINDING SITE FOR RESIDUE SO4 A 185
12
CC3
SOFTWARE
ARG A:1064 , GLU A:1114 , THR A:1290 , GLU A:1291 , HOH A:8395 , HIS B:2284 , GLN B:2288
BINDING SITE FOR RESIDUE SO4 A 284
13
CC4
SOFTWARE
PRO A:1062 , HOH A:8673 , HIS B:2284 , ARG B:2287
BINDING SITE FOR RESIDUE SO4 B 285
14
CC5
SOFTWARE
HIS C:3284 , ARG C:3287 , HOH C:8206
BINDING SITE FOR RESIDUE SO4 C 384
15
CC6
SOFTWARE
GLU B:2114 , THR B:2290 , GLU B:2291 , HOH B:8361 , HIS C:3284 , GLN C:3288
BINDING SITE FOR RESIDUE SO4 B 385
16
DC4
SOFTWARE
GLY A:1141 , GLY A:1142 , GLY A:1143 , SER A:1221 , ALA A:1222 , LEU A:1304 , MET A:1425 , HIS A:1468
BINDING SITE FOR RESIDUE GD7 A 1
17
DC5
SOFTWARE
GLY B:2141 , GLY B:2142 , GLY B:2143 , SER B:2221 , ALA B:2222 , LEU B:2304 , ILE B:2359 , MET B:2425 , HIS B:2468
BINDING SITE FOR RESIDUE GD7 B 1
18
DC6
SOFTWARE
GLY C:3141 , GLY C:3142 , GLY C:3143 , SER C:3221 , ALA C:3222 , LEU C:3304 , ILE C:3359 , MET C:3425 , PHE C:3426 , HIS C:3468
BINDING SITE FOR RESIDUE GD7 C 1
[
close Site info
]
SAPs(SNPs)/Variants
(4, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_014314 (S6075N, chain A/B/C/D/E/A/B/C, )
2: VAR_046954 (G6143E, chain A/B/C/D/E/A/B/C, )
3: VAR_014594 (R6199H, chain A/B/C/D/E/A/B/C, )
4: VAR_014595 (D6203E, chain A/B/C/D/E/A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_014314
S
75
N
EST1_HUMAN
Polymorphism
2307240
A
B
C
D
E
A/B/C
S
1075
2075
3075
4075
5075
6075
N
2
UniProt
VAR_046954
G
143
E
EST1_HUMAN
Polymorphism
71647871
A
B
C
D
E
A/B/C
G
1143
2143
3143
4143
5143
6143
E
3
UniProt
VAR_014594
R
199
H
EST1_HUMAN
Polymorphism
2307243
A
B
C
D
E
A/B/C
R
1199
2199
3199
4199
5199
6199
H
4
UniProt
VAR_014595
D
203
E
EST1_HUMAN
Polymorphism
2307227
A
B
C
D
E
A/B/C
D
1203
2203
3203
4203
5203
6203
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: CARBOXYLESTERASE_B_2 (A:1114-1124,B:2114-2124,C:3114-312...)
2: CARBOXYLESTERASE_B_1 (A:1208-1223,B:2208-2223,C:3208-322...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CARBOXYLESTERASE_B_2
PS00941
Carboxylesterases type-B signature 2.
EST1_HUMAN
114-124
3
A:1114-1124
B:2114-2124
C:3114-3124
-
-
-
2
CARBOXYLESTERASE_B_1
PS00122
Carboxylesterases type-B serine active site.
EST1_HUMAN
208-223
3
A:1208-1223
B:2208-2223
C:3208-3223
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2hrqa_ (A:)
1b: SCOP_d2hrqb_ (B:)
1c: SCOP_d2hrqc_ (C:)
1d: SCOP_d2hrqd_ (D:)
1e: SCOP_d2hrqe_ (E:)
1f: SCOP_d2hrqf_ (F:)
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
Acetylcholinesterase-like
(219)
Protein domain
:
automated matches
(91)
Human (Homo sapiens) [TaxId: 9606]
(35)
1a
d2hrqa_
A:
1b
d2hrqb_
B:
1c
d2hrqc_
C:
1d
d2hrqd_
D:
1e
d2hrqe_
E:
1f
d2hrqf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2hrqB00 (B:2022-2553)
1b: CATH_2hrqC00 (C:3022-3553)
1c: CATH_2hrqE00 (E:5022-5553)
1d: CATH_2hrqF00 (F:6022-6553)
1e: CATH_2hrqA00 (A:1021-1553)
1f: CATH_2hrqD00 (D:4021-4553)
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Classes
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1820, no name defined]
(692)
Human (Homo sapiens)
(118)
1a
2hrqB00
B:2022-2553
1b
2hrqC00
C:3022-3553
1c
2hrqE00
E:5022-5553
1d
2hrqF00
F:6022-6553
1e
2hrqA00
A:1021-1553
1f
2hrqD00
D:4021-4553
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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