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1DO8
Asym. Unit
Info
Asym.Unit (391 KB)
Biol.Unit 1 (379 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME
Authors
:
Z. Yang, D. L. Floyd, G. Loeber, L. Tong
Date
:
19 Dec 99 (Deposition) - 06 Mar 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidative Decarboxylase, Four Domains: One With Rossmann Fold, One With Parallel Alpha-Beta Fold, One Mostly Helical, And One Mostly Extended, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Yang, D. L. Floyd, G. Loeber, L. Tong
Structure Of A Closed Form Of Human Malic Enzyme And Implications For Catalytic Mechanism.
Nat. Struct. Biol. V. 7 251 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 72)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2ao: SELENOMETHIONINE (MSEao)
2ap: SELENOMETHIONINE (MSEap)
2aq: SELENOMETHIONINE (MSEaq)
2ar: SELENOMETHIONINE (MSEar)
2as: SELENOMETHIONINE (MSEas)
2at: SELENOMETHIONINE (MSEat)
2au: SELENOMETHIONINE (MSEau)
2av: SELENOMETHIONINE (MSEav)
2aw: SELENOMETHIONINE (MSEaw)
2ax: SELENOMETHIONINE (MSEax)
2ay: SELENOMETHIONINE (MSEay)
2az: SELENOMETHIONINE (MSEaz)
2b: SELENOMETHIONINE (MSEb)
2ba: SELENOMETHIONINE (MSEba)
2bb: SELENOMETHIONINE (MSEbb)
2bc: SELENOMETHIONINE (MSEbc)
2bd: SELENOMETHIONINE (MSEbd)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
3e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
3f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
3g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
3h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
4a: OXALATE ION (OXLa)
4b: OXALATE ION (OXLb)
4c: OXALATE ION (OXLc)
4d: OXALATE ION (OXLd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
4
Ligand/Ion
MANGANESE (II) ION
2
MSE
56
Mod. Amino Acid
SELENOMETHIONINE
3
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4
OXL
4
Ligand/Ion
OXALATE ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:112 , ARG A:165 , LEU A:167 , LYS A:183 , GLU A:255 , ASP A:256 , ASP A:279 , ASN A:421 , ASN A:466 , ASN A:467 , NAD A:601 , MN A:604 , HOH A:4290
BINDING SITE FOR RESIDUE OXL A 603
02
AC2
SOFTWARE
ARG A:165 , GLU A:255 , ASP A:256 , ASP A:279 , OXL A:603 , HOH A:606
BINDING SITE FOR RESIDUE MN A 604
03
AC3
SOFTWARE
ARG B:1165 , LEU B:1167 , LYS B:1183 , GLU B:1255 , ASP B:1256 , ASP B:1279 , ASN B:1421 , ASN B:1466 , ASN B:1467 , NAD B:1601 , MN B:1604 , HOH B:4112
BINDING SITE FOR RESIDUE OXL B 1603
04
AC4
SOFTWARE
ARG B:1165 , GLU B:1255 , ASP B:1256 , ASP B:1279 , OXL B:1603 , HOH B:1606
BINDING SITE FOR RESIDUE MN B 1604
05
AC5
SOFTWARE
ARG C:2165 , LEU C:2167 , LYS C:2183 , GLU C:2255 , ASP C:2256 , ASP C:2279 , ASN C:2421 , ASN C:2466 , ASN C:2467 , NAD C:2601 , MN C:2604 , HOH C:4054
BINDING SITE FOR RESIDUE OXL C 2603
06
AC6
SOFTWARE
ARG C:2165 , GLU C:2255 , ASP C:2256 , ASP C:2279 , OXL C:2603 , HOH C:2606
BINDING SITE FOR RESIDUE MN C 2604
07
AC7
SOFTWARE
ARG D:3165 , LEU D:3167 , LYS D:3183 , GLU D:3255 , ASP D:3256 , ASP D:3279 , ASN D:3421 , ASN D:3466 , ASN D:3467 , NAD D:3601 , MN D:3604 , HOH D:4119
BINDING SITE FOR RESIDUE OXL D 3603
08
AC8
SOFTWARE
ARG D:3165 , GLU D:3255 , ASP D:3256 , ASP D:3279 , OXL D:3603 , HOH D:3606
BINDING SITE FOR RESIDUE MN D 3604
09
AC9
SOFTWARE
ARG A:165 , LEU A:167 , GLY A:168 , ASN A:259 , ASP A:279 , THR A:283 , GLY A:311 , ALA A:312 , GLY A:313 , GLU A:314 , ALA A:315 , ASP A:345 , LYS A:346 , VAL A:392 , ALA A:393 , GLY A:394 , ALA A:395 , LEU A:398 , LEU A:419 , ASN A:421 , GLY A:446 , GLY A:465 , ASN A:466 , ASN A:467 , OXL A:603 , HOH A:4007 , HOH A:4315
BINDING SITE FOR RESIDUE NAD A 601
10
BC1
SOFTWARE
HIS A:154 , ARG A:194 , ARG A:197 , ILE A:479 , LEU A:480 , ARG A:542 , TYR A:552 , ARG A:556 , HOH A:4739 , HOH A:4888 , ASP D:3244 , ARG D:3245 , GLY D:3247
BINDING SITE FOR RESIDUE NAD A 602
11
BC2
SOFTWARE
ARG B:1165 , LEU B:1167 , GLY B:1168 , ASN B:1259 , THR B:1283 , GLY B:1311 , ALA B:1312 , GLY B:1313 , GLU B:1314 , ALA B:1315 , ASP B:1345 , LYS B:1346 , VAL B:1392 , ALA B:1393 , GLY B:1394 , LEU B:1398 , LEU B:1419 , ASN B:1421 , GLY B:1446 , GLY B:1465 , ASN B:1466 , ASN B:1467 , OXL B:1603 , HOH B:4066 , HOH B:4933
BINDING SITE FOR RESIDUE NAD B 1601
12
BC3
SOFTWARE
HIS B:1154 , LYS B:1156 , GLY B:1192 , ARG B:1194 , ARG B:1197 , ILE B:1479 , LEU B:1480 , ARG B:1542 , ARG B:1556 , HOH B:4443 , ARG C:2245
BINDING SITE FOR RESIDUE NAD B 1602
13
BC4
SOFTWARE
ARG C:2165 , LEU C:2167 , GLY C:2168 , ASN C:2259 , ASP C:2279 , THR C:2283 , GLY C:2311 , ALA C:2312 , GLY C:2313 , GLU C:2314 , ALA C:2315 , ASP C:2345 , LYS C:2346 , VAL C:2392 , ALA C:2393 , GLY C:2394 , ALA C:2395 , LEU C:2419 , ASN C:2421 , GLY C:2446 , GLY C:2465 , ASN C:2466 , ASN C:2467 , OXL C:2603 , HOH C:4017 , HOH C:4175 , HOH C:4678
BINDING SITE FOR RESIDUE NAD C 2601
14
BC5
SOFTWARE
ARG B:1245 , HOH B:4632 , HIS C:2154 , LYS C:2156 , GLY C:2192 , ILE C:2193 , ARG C:2194 , ARG C:2197 , ILE C:2479 , LEU C:2480 , ARG C:2542 , TYR C:2552 , ARG C:2556 , HOH C:4303
BINDING SITE FOR RESIDUE NAD C 2602
15
BC6
SOFTWARE
ARG D:3165 , LEU D:3167 , GLY D:3168 , ASN D:3259 , ASP D:3279 , THR D:3283 , GLY D:3311 , ALA D:3312 , GLY D:3313 , GLU D:3314 , ALA D:3315 , ASP D:3345 , LYS D:3346 , VAL D:3392 , ALA D:3393 , GLY D:3394 , ALA D:3395 , LEU D:3398 , LEU D:3419 , ASN D:3421 , GLY D:3446 , GLY D:3465 , ASN D:3466 , ASN D:3467 , OXL D:3603 , HOH D:4124 , HOH D:4485 , HOH D:4533 , HOH D:4788
BINDING SITE FOR RESIDUE NAD D 3601
16
BC7
SOFTWARE
ASP A:244 , ARG A:245 , HIS D:3154 , ARG D:3194 , ARG D:3197 , ILE D:3479 , LEU D:3480 , ASN D:3482 , ARG D:3542 , TYR D:3552 , ARG D:3556
BINDING SITE FOR RESIDUE NAD D 3602
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_034104 (P3114L, chain A/B/C/D, )
2: VAR_050017 (G3450E, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_034104
P
114
L
MAOM_HUMAN
Polymorphism
16952692
A
B
C
D
P
114
1114
2114
3114
L
2
UniProt
VAR_050017
G
450
E
MAOM_HUMAN
Polymorphism
649224
A
B
C
D
G
450
1450
2450
3450
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: MALIC_ENZYMES (A:276-292,B:1276-1292,C:2276-2292,...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MALIC_ENZYMES
PS00331
Malic enzymes signature.
MAOM_HUMAN
276-292
4
A:276-292
B:1276-1292
C:2276-2292
D:3276-3292
[
close PROSITE info
]
Exons
(15, 60)
Info
All Exons
Exon 1.2 (A:21-36 | B:1021-1036 | C:2021-203...)
Exon 1.3 (A:37-81 | B:1037-1081 | C:2037-208...)
Exon 1.4 (A:81-131 | B:1081-1131 | C:2081-21...)
Exon 1.5 (A:131-156 | B:1131-1156 | C:2131-2...)
Exon 1.6 (A:157-210 | B:1157-1210 | C:2157-2...)
Exon 1.7 (A:211-245 | B:1211-1245 | C:2211-2...)
Exon 1.8 (A:245-282 | B:1245-1282 | C:2245-2...)
Exon 1.9 (A:282-314 | B:1282-1314 | C:2282-2...)
Exon 1.10 (A:315-352 | B:1315-1352 | C:2315-2...)
Exon 1.11 (A:353-391 | B:1353-1391 | C:2353-2...)
Exon 1.12 (A:391-438 | B:1391-1438 | C:2391-2...)
Exon 1.13 (A:439-473 | B:1439-1473 | C:2439-2...)
Exon 1.14 (A:473-496 | B:1473-1496 | C:2473-2...)
Exon 1.15 (A:497-529 | B:1497-1529 | C:2497-2...)
Exon 1.16b (A:530-573 | B:1530-1573 | C:2530-2...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16b
16: Boundary 1.16b/-
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
1.1a
ENST00000321341
1a
ENSE00001948888
chr18:
48405419-48405678
260
MAOM_HUMAN
-
0
0
-
-
1.2
ENST00000321341
2
ENSE00001222938
chr18:
48422179-48422298
120
MAOM_HUMAN
1-36
36
4
A:21-36
B:1021-1036
C:2021-2036
D:3021-3036
16
16
16
16
1.3
ENST00000321341
3
ENSE00000996845
chr18:
48434433-48434566
134
MAOM_HUMAN
37-81
45
4
A:37-81
B:1037-1081
C:2037-2081
D:3037-3081
45
45
45
45
1.4
ENST00000321341
4
ENSE00000996846
chr18:
48439171-48439320
150
MAOM_HUMAN
81-131
51
4
A:81-131
B:1081-1131
C:2081-2131
D:3081-3131
51
51
51
51
1.5
ENST00000321341
5
ENSE00001151659
chr18:
48442538-48442613
76
MAOM_HUMAN
131-156
26
4
A:131-156
B:1131-1156
C:2131-2156
D:3131-3156
26
26
26
26
1.6
ENST00000321341
6
ENSE00001151654
chr18:
48443717-48443878
162
MAOM_HUMAN
157-210
54
4
A:157-210
B:1157-1210
C:2157-2210
D:3157-3210
54
54
54
54
1.7
ENST00000321341
7
ENSE00001151650
chr18:
48444480-48444583
104
MAOM_HUMAN
211-245
35
4
A:211-245
B:1211-1245
C:2211-2245
D:3211-3245
35
35
35
35
1.8
ENST00000321341
8
ENSE00001151645
chr18:
48446826-48446935
110
MAOM_HUMAN
245-282
38
4
A:245-282
B:1245-1282
C:2245-2282
D:3245-3282
38
38
38
38
1.9
ENST00000321341
9
ENSE00001151639
chr18:
48447031-48447128
98
MAOM_HUMAN
282-314
33
4
A:282-314
B:1282-1314
C:2282-2314
D:3282-3314
33
33
33
33
1.10
ENST00000321341
10
ENSE00001151634
chr18:
48447444-48447557
114
MAOM_HUMAN
315-352
38
4
A:315-352
B:1315-1352
C:2315-2352
D:3315-3352
38
38
38
38
1.11
ENST00000321341
11
ENSE00000950181
chr18:
48450468-48450582
115
MAOM_HUMAN
353-391
39
4
A:353-391
B:1353-1391
C:2353-2391
D:3353-3391
39
39
39
39
1.12
ENST00000321341
12
ENSE00000950182
chr18:
48452126-48452268
143
MAOM_HUMAN
391-438
48
4
A:391-438
B:1391-1438
C:2391-2438
D:3391-3438
48
48
48
48
1.13
ENST00000321341
13
ENSE00000950183
chr18:
48458628-48458730
103
MAOM_HUMAN
439-473
35
4
A:439-473
B:1439-1473
C:2439-2473
D:3439-3473
35
35
35
35
1.14
ENST00000321341
14
ENSE00000950184
chr18:
48465940-48466010
71
MAOM_HUMAN
473-496
24
4
A:473-496
B:1473-1496
C:2473-2496
D:3473-3496
24
24
24
24
1.15
ENST00000321341
15
ENSE00000950185
chr18:
48466658-48466756
99
MAOM_HUMAN
497-529
33
4
A:497-529
B:1497-1529
C:2497-2529
D:3497-3529
33
33
33
33
1.16b
ENST00000321341
16b
ENSE00001605064
chr18:
48473387-48474691
1305
MAOM_HUMAN
530-584
55
4
A:530-573
B:1530-1573
C:2530-2573
D:3530-3573
44
44
44
44
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1do8a2 (A:21-279)
1b: SCOP_d1do8b4 (B:1021-1279)
1c: SCOP_d1do8c4 (C:2021-2279)
1d: SCOP_d1do8d4 (D:3021-3279)
2a: SCOP_d1do8a1 (A:280-573)
2b: SCOP_d1do8b3 (B:1280-1573)
2c: SCOP_d1do8c3 (C:2280-2573)
2d: SCOP_d1do8d3 (D:3280-3573)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Malic enzyme N-domain
(14)
Protein domain
:
Mitochondrial NAD(P)-dependent malic enzyme
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
1a
d1do8a2
A:21-279
1b
d1do8b4
B:1021-1279
1c
d1do8c4
C:2021-2279
1d
d1do8d4
D:3021-3279
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Mitochondrial NAD(P)-dependent malic enzyme
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
2a
d1do8a1
A:280-573
2b
d1do8b3
B:1280-1573
2c
d1do8c3
C:2280-2573
2d
d1do8d3
D:3280-3573
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1do8A01 (A:21-277)
1b: CATH_1do8B01 (B:1021-1277)
1c: CATH_1do8C01 (C:2021-2277)
1d: CATH_1do8D01 (D:3021-3277)
2a: CATH_1do8A02 (A:278-573)
2b: CATH_1do8B02 (B:1278-1573)
2c: CATH_1do8C02 (C:2278-2573)
2d: CATH_1do8D02 (D:3278-3573)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain. Chain A
(17)
Human (Homo sapiens)
(11)
1a
1do8A01
A:21-277
1b
1do8B01
B:1021-1277
1c
1do8C01
C:2021-2277
1d
1do8D01
D:3021-3277
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
1do8A02
A:278-573
2b
1do8B02
B:1278-1573
2c
1do8C02
C:2278-2573
2d
1do8D02
D:3278-3573
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