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2GRA
Asym. Unit
Info
Asym.Unit (234 KB)
Biol.Unit 1 (49 KB)
Biol.Unit 2 (48 KB)
Biol.Unit 3 (49 KB)
Biol.Unit 4 (49 KB)
Biol.Unit 5 (50 KB)
Biol.Unit 6 (94 KB)
Biol.Unit 7 (94 KB)
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Title
:
CRYSTAL STRUCTURE OF HUMAN PYRROLINE-5-CARBOXYLATE REDUCTASE COMPLEXED WITH NADP
Authors
:
Z. Meng, Z. Lou, Z. Liu, Z. Rao
Date
:
23 Apr 06 (Deposition) - 03 Oct 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: D,E (1x)
Biol. Unit 7: A,C (1x)
Keywords
:
Human Pyrroline-5-Carboxylate Reductase, Nadph, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Meng, Z. Lou, Z. Liu, M. Li, X. Zhao, M. Bartlam, Z. Rao
Crystal Structure Of Human Pyrroline-5-Carboxylate Reductas
J. Mol. Biol. V. 359 1364 2006
[
close entry info
]
Hetero Components
(2, 10)
Info
All Hetero Components
1a: GLUTAMIC ACID (GLUa)
1b: GLUTAMIC ACID (GLUb)
1c: GLUTAMIC ACID (GLUc)
1d: GLUTAMIC ACID (GLUd)
1e: GLUTAMIC ACID (GLUe)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
2d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
2e: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GLU
5
Mod. Amino Acid
GLUTAMIC ACID
2
NAP
5
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:129 , GLU A:130 , SER A:154 , SER A:155 , GLY A:157 , PHE A:158 , LEU A:217 , LEU A:218 , HIS A:219 , SER A:220 , GLU A:1301 , LEU C:201 , ARG C:204 , GLN C:208
BINDING SITE FOR RESIDUE NAP A 1300
02
AC2
SOFTWARE
NAP A:1300
BINDING SITE FOR RESIDUE GLU A 1301
03
AC3
SOFTWARE
ARG B:129 , GLU B:130 , SER B:154 , SER B:155 , VAL B:156 , GLY B:157 , PHE B:158 , ARG B:200 , LEU B:201 , ARG B:204 , GLN B:208 , LEU B:217 , LEU B:218 , HIS B:219 , GLU B:221 , GLU B:2301 , HOH B:2319 , HOH B:2338 , HOH B:2345 , HOH B:2362 , HOH B:2364 , HOH B:2395
BINDING SITE FOR RESIDUE NAP B 2300
04
AC4
SOFTWARE
ARG B:129 , NAP B:2300
BINDING SITE FOR RESIDUE GLU B 2301
05
AC5
SOFTWARE
ARG A:200 , LEU A:201 , ARG A:204 , GLN A:208 , ARG C:129 , GLU C:130 , SER C:154 , SER C:155 , VAL C:156 , GLY C:157 , PHE C:158 , LEU C:218 , SER C:220 , GLU C:3301 , HOH C:3320 , HOH C:3394
BINDING SITE FOR RESIDUE NAP C 3300
06
AC6
SOFTWARE
NAP C:3300
BINDING SITE FOR RESIDUE GLU C 3301
07
AC7
SOFTWARE
GLU D:130 , SER D:154 , SER D:155 , GLY D:157 , PHE D:158 , LEU D:217 , LEU D:218 , HIS D:219 , SER D:220 , GLU D:221 , GLU D:4301 , HOH D:4315 , ARG E:200 , LEU E:201 , ARG E:204 , GLN E:208 , HOH E:5318
BINDING SITE FOR RESIDUE NAP D 4300
08
AC8
SOFTWARE
NAP D:4300
BINDING SITE FOR RESIDUE GLU D 4301
09
AC9
SOFTWARE
ARG D:200 , LEU D:201 , ARG D:204 , GLN D:208 , ARG E:129 , GLU E:130 , SER E:154 , GLY E:157 , PHE E:158 , LEU E:217 , LEU E:218 , HIS E:219 , GLU E:221 , GLU E:5301 , HOH E:5448 , HOH E:5451
BINDING SITE FOR RESIDUE NAP E 5300
10
BC1
SOFTWARE
NAP E:5300
BINDING SITE FOR RESIDUE GLU E 5301
[
close Site info
]
SAPs(SNPs)/Variants
(10, 50)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_059068 (R119G, chain A/B/C/D/E, )
02: VAR_059069 (R119H, chain A/B/C/D/E, )
03: VAR_059070 (A179T, chain A/B/C/D/E, )
04: VAR_059071 (A189V, chain A/B/C/D/E, )
05: VAR_059072 (G206R, chain A/B/C/D/E, )
06: VAR_059073 (G206W, chain A/B/C/D/E, )
07: VAR_067600 (G248E, chain A/B/C/D/E, )
08: VAR_059074 (R251H, chain A/B/C/D/E, )
09: VAR_059075 (A257T, chain A/B/C/D/E, )
10: VAR_059076 (R266Q, chain A/B/C/D/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_059068
R
119
G
P5CR1_HUMAN
Disease (ARCL2B)
---
A/B/C/D/E
R
119
G
02
UniProt
VAR_059069
R
119
H
P5CR1_HUMAN
Disease (ARCL2B)
121918377
A/B/C/D/E
R
119
H
03
UniProt
VAR_059070
A
179
T
P5CR1_HUMAN
Disease (ARCL2B)
---
A/B/C/D/E
A
179
T
04
UniProt
VAR_059071
A
189
V
P5CR1_HUMAN
Polymorphism
---
A/B/C/D/E
A
189
V
05
UniProt
VAR_059072
G
206
R
P5CR1_HUMAN
Disease (ARCL2B)
121918375
A/B/C/D/E
G
206
R
06
UniProt
VAR_059073
G
206
W
P5CR1_HUMAN
Disease (ARCL2B)
---
A/B/C/D/E
G
206
W
07
UniProt
VAR_067600
G
248
E
P5CR1_HUMAN
Disease (ARCL3B)
281875319
A/B/C/D/E
G
248
E
08
UniProt
VAR_059074
R
251
H
P5CR1_HUMAN
Disease (ARCL3B)
---
A/B/C/D/E
R
251
H
09
UniProt
VAR_059075
A
257
T
P5CR1_HUMAN
Disease (ARCL3B)
281875318
A/B/C/D/E
A
257
T
10
UniProt
VAR_059076
R
266
Q
P5CR1_HUMAN
Disease (ARCL2B)
---
A/B/C/D/E
R
266
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 5)
Info
All PROSITE Patterns/Profiles
1: P5CR (A:224-246,B:224-246,C:224-246,D:22...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
P5CR
PS00521
Delta 1-pyrroline-5-carboxylate reductase signature.
P5CR1_HUMAN
224-246
5
A:224-246
B:224-246
C:224-246
D:224-246
E:224-246
[
close PROSITE info
]
Exons
(7, 35)
Info
All Exons
Exon 1.3a (A:1-23 | B:1-23 | C:1-23 | D:1-23 ...)
Exon 1.4 (A:23-46 | B:23-46 | C:23-46 | D:23...)
Exon 1.5 (A:47-106 | B:47-106 (gaps) | C:47-...)
Exon 1.6 (A:107-180 | B:107-180 | C:107-180 ...)
Exon 1.7 (A:181-211 | B:181-211 | C:181-211 ...)
Exon 1.8b (A:212-266 | B:212-266 | C:212-266 ...)
Exon 1.9b (A:266-275 | B:266-275 | C:266-275 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.3a
2: Boundary 1.3a/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6
5: Boundary 1.6/1.7
6: Boundary 1.7/1.8b
7: Boundary 1.8b/1.9b
8: Boundary 1.9b/-
View:
Label:
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
1.3a
ENST00000329875
3a
ENSE00001511592
chr17:
79894968-79894624
345
P5CR1_HUMAN
1-23
23
5
A:1-23
B:1-23
C:1-23
D:1-23
E:1-23
23
23
23
23
23
1.4
ENST00000329875
4
ENSE00001321886
chr17:
79894069-79893999
71
P5CR1_HUMAN
23-46
24
5
A:23-46
B:23-46
C:23-46
D:23-46
E:23-46
24
24
24
24
24
1.5
ENST00000329875
5
ENSE00001609318
chr17:
79893392-79893213
180
P5CR1_HUMAN
47-106
60
5
A:47-106
B:47-106 (gaps)
C:47-106
D:47-106
E:47-106
60
60
60
60
60
1.6
ENST00000329875
6
ENSE00001295081
chr17:
79893023-79892802
222
P5CR1_HUMAN
107-180
74
5
A:107-180
B:107-180
C:107-180
D:107-180
E:107-180
74
74
74
74
74
1.7
ENST00000329875
7
ENSE00001652123
chr17:
79892621-79892529
93
P5CR1_HUMAN
181-211
31
5
A:181-211
B:181-211
C:181-211
D:181-211
E:181-211
31
31
31
31
31
1.8b
ENST00000329875
8b
ENSE00001731739
chr17:
79892365-79892202
164
P5CR1_HUMAN
212-266
55
5
A:212-266
B:212-266
C:212-266
D:212-266
E:212-266
55
55
55
55
55
1.9b
ENST00000329875
9b
ENSE00001665866
chr17:
79891252-79890269
984
P5CR1_HUMAN
266-319
54
5
A:266-275
B:266-275
C:266-275
D:266-275
E:266-275
10
10
10
10
10
[
close EXON info
]
SCOP Domains
(2, 10)
Info
All SCOP Domains
1a: SCOP_d2graa2 (A:165-275)
1b: SCOP_d2grab2 (B:165-275)
1c: SCOP_d2grac2 (C:165-275)
1d: SCOP_d2grad2 (D:165-275)
1e: SCOP_d2grae2 (E:165-275)
2a: SCOP_d2graa1 (A:-1-164)
2b: SCOP_d2grab1 (B:-1-164)
2c: SCOP_d2grac1 (C:-1-164)
2d: SCOP_d2grad1 (D:-1-164)
2e: SCOP_d2grae1 (E:-1-164)
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(
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(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d2graa2
A:165-275
1b
d2grab2
B:165-275
1c
d2grac2
C:165-275
1d
d2grad2
D:165-275
1e
d2grae2
E:165-275
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Human (Homo sapiens) [TaxId: 9606]
(32)
2a
d2graa1
A:-1-164
2b
d2grab1
B:-1-164
2c
d2grac1
C:-1-164
2d
d2grad1
D:-1-164
2e
d2grae1
E:-1-164
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Asym.Unit (234 KB)
Header - Asym.Unit
Biol.Unit 1 (49 KB)
Header - Biol.Unit 1
Biol.Unit 2 (48 KB)
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Biol.Unit 3 (49 KB)
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Biol.Unit 4 (49 KB)
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