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1EYB
Asym. Unit
Info
Asym.Unit (83 KB)
Biol.Unit 1 (454 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF APO HUMAN HOMOGENTISATE DIOXYGENASE
Authors
:
D. E. Timm, G. P. Titus, M. A. Penalva, H. A. Mueller, S. M. De Cordoba
Date
:
05 May 00 (Deposition) - 05 Nov 00 (Release) - 24 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (6x)
Keywords
:
Jelly Roll, Beta Sandwich, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. P. Titus, H. A. Mueller, J. Burgner, S. Rodriguez De Cordoba, M. A. Penalva, D. E. Timm
Crystal Structure Of Human Homogentisate Dioxygenase.
Nat. Struct. Biol. V. 7 542 2000
[
close entry info
]
Hetero Components
(1, 9)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
9
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(70, 70)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_073076 (E3A, chain A, )
02: VAR_073077 (E13K, chain A, )
03: VAR_073078 (D18N, chain A, )
04: VAR_009618 (L25P, chain A, )
05: VAR_073079 (Q33R, chain A, )
06: VAR_005272 (E42A, chain A, )
07: VAR_073080 (L44F, chain A, )
08: VAR_073081 (R53Q, chain A, )
09: VAR_005273 (W60G, chain A, )
10: VAR_073082 (L61P, chain A, )
11: VAR_005274 (Y62C, chain A, )
12: VAR_073083 (F73L, chain A, )
13: VAR_049353 (H80H, chain A, )
14: VAR_073084 (P92T, chain A, )
15: VAR_005275 (W97G, chain A, )
16: VAR_073085 (W97R, chain A, )
17: VAR_073086 (G115R, chain A, )
18: VAR_073087 (L116P, chain A, )
19: VAR_073088 (C120F, chain A, )
20: VAR_073089 (C120W, chain A, )
21: VAR_005276 (A122D, chain A, )
22: VAR_073090 (A122V, chain A, )
23: VAR_073091 (G123A, chain A, )
24: VAR_073092 (G123R, chain A, )
25: VAR_073093 (L137P, chain A, )
26: VAR_073094 (G152A, chain A, )
27: VAR_005277 (D153G, chain A, )
28: VAR_073095 (P158L, chain A, )
29: VAR_005278 (G161R, chain A, )
30: VAR_073096 (E168D, chain A, )
31: VAR_009619 (E168K, chain A, )
32: VAR_073097 (F169L, chain A, )
33: VAR_073098 (K171N, chain A, )
34: VAR_073099 (M172T, chain A, )
35: VAR_073100 (E178G, chain A, )
36: VAR_073101 (Q183R, chain A, )
37: VAR_073102 (R187G, chain A, )
38: VAR_005279 (S189I, chain A, )
39: VAR_073103 (R197G, chain A, )
40: VAR_005280 (I216T, chain A, )
41: VAR_073104 (G217W, chain A, )
42: VAR_073105 (N219S, chain A, )
43: VAR_005281 (R225H, chain A, )
44: VAR_073106 (R225L, chain A, )
45: VAR_073107 (R225P, chain A, )
46: VAR_005282 (F227S, chain A, )
47: VAR_005283 (P230S, chain A, )
48: VAR_005284 (P230T, chain A, )
49: VAR_073108 (V245F, chain A, )
50: VAR_073109 (Q258P, chain A, )
51: VAR_073110 (H269R, chain A, )
52: VAR_009620 (G270R, chain A, )
53: VAR_073111 (K276N, chain A, )
54: VAR_005285 (D291E, chain A, )
55: VAR_005286 (V300G, chain A, )
56: VAR_073112 (R321P, chain A, )
57: VAR_073113 (F329C, chain A, )
58: VAR_008744 (R330S, chain A, )
59: VAR_073114 (N337D, chain A, )
60: VAR_073115 (P359L, chain A, )
61: VAR_073116 (G360A, chain A, )
62: VAR_073117 (G360R, chain A, )
63: VAR_073118 (G361R, chain A, )
64: VAR_073119 (G362E, chain A, )
65: VAR_005287 (M368V, chain A, )
66: VAR_073120 (T369N, chain A, )
67: VAR_008745 (H371R, chain A, )
68: VAR_073121 (P373L, chain A, )
69: VAR_073122 (D374H, chain A, )
70: VAR_073123 (E401Q, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_073076
E
3
A
HGD_HUMAN
Disease (AKU)
---
A
E
3
A
02
UniProt
VAR_073077
E
13
K
HGD_HUMAN
Disease (AKU)
---
A
E
13
K
03
UniProt
VAR_073078
D
18
N
HGD_HUMAN
Disease (AKU)
---
A
D
18
N
04
UniProt
VAR_009618
L
25
P
HGD_HUMAN
Disease (AKU)
---
A
L
25
P
05
UniProt
VAR_073079
Q
33
R
HGD_HUMAN
Disease (AKU)
---
A
Q
33
R
06
UniProt
VAR_005272
E
42
A
HGD_HUMAN
Disease (AKU)
---
A
E
42
A
07
UniProt
VAR_073080
L
44
F
HGD_HUMAN
Disease (AKU)
---
A
L
44
F
08
UniProt
VAR_073081
R
53
Q
HGD_HUMAN
Disease (AKU)
---
A
R
53
Q
09
UniProt
VAR_005273
W
60
G
HGD_HUMAN
Disease (AKU)
---
A
W
60
G
10
UniProt
VAR_073082
L
61
P
HGD_HUMAN
Disease (AKU)
---
A
L
61
P
11
UniProt
VAR_005274
Y
62
C
HGD_HUMAN
Disease (AKU)
---
A
Y
62
C
12
UniProt
VAR_073083
F
73
L
HGD_HUMAN
Disease (AKU)
---
A
F
73
L
13
UniProt
VAR_049353
Q
80
H
HGD_HUMAN
Polymorphism
2255543
A
H
80
H
14
UniProt
VAR_073084
P
92
T
HGD_HUMAN
Disease (AKU)
---
A
P
92
T
15
UniProt
VAR_005275
W
97
G
HGD_HUMAN
Disease (AKU)
---
A
W
97
G
16
UniProt
VAR_073085
W
97
R
HGD_HUMAN
Disease (AKU)
---
A
W
97
R
17
UniProt
VAR_073086
G
115
R
HGD_HUMAN
Disease (AKU)
---
A
G
115
R
18
UniProt
VAR_073087
L
116
P
HGD_HUMAN
Disease (AKU)
---
A
L
116
P
19
UniProt
VAR_073088
C
120
F
HGD_HUMAN
Disease (AKU)
---
A
C
120
F
20
UniProt
VAR_073089
C
120
W
HGD_HUMAN
Disease (AKU)
---
A
C
120
W
21
UniProt
VAR_005276
A
122
D
HGD_HUMAN
Disease (AKU)
---
A
A
122
D
22
UniProt
VAR_073090
A
122
V
HGD_HUMAN
Disease (AKU)
---
A
A
122
V
23
UniProt
VAR_073091
G
123
A
HGD_HUMAN
Disease (AKU)
---
A
G
123
A
24
UniProt
VAR_073092
G
123
R
HGD_HUMAN
Disease (AKU)
---
A
G
123
R
25
UniProt
VAR_073093
L
137
P
HGD_HUMAN
Disease (AKU)
---
A
L
137
P
26
UniProt
VAR_073094
G
152
A
HGD_HUMAN
Disease (AKU)
---
A
G
152
A
27
UniProt
VAR_005277
D
153
G
HGD_HUMAN
Disease (AKU)
---
A
D
153
G
28
UniProt
VAR_073095
P
158
L
HGD_HUMAN
Disease (AKU)
---
A
P
158
L
29
UniProt
VAR_005278
G
161
R
HGD_HUMAN
Disease (AKU)
28941783
A
G
161
R
30
UniProt
VAR_073096
E
168
D
HGD_HUMAN
Disease (AKU)
---
A
E
168
D
31
UniProt
VAR_009619
E
168
K
HGD_HUMAN
Disease (AKU)
---
A
E
168
K
32
UniProt
VAR_073097
F
169
L
HGD_HUMAN
Disease (AKU)
---
A
F
169
L
33
UniProt
VAR_073098
K
171
N
HGD_HUMAN
Disease (AKU)
---
A
K
171
N
34
UniProt
VAR_073099
M
172
T
HGD_HUMAN
Polymorphism
---
A
M
172
T
35
UniProt
VAR_073100
E
178
G
HGD_HUMAN
Disease (AKU)
---
A
E
178
G
36
UniProt
VAR_073101
Q
183
R
HGD_HUMAN
Disease (AKU)
---
A
Q
183
R
37
UniProt
VAR_073102
R
187
G
HGD_HUMAN
Disease (AKU)
---
A
R
187
G
38
UniProt
VAR_005279
S
189
I
HGD_HUMAN
Disease (AKU)
---
A
S
189
I
39
UniProt
VAR_073103
R
197
G
HGD_HUMAN
Disease (AKU)
---
A
R
197
G
40
UniProt
VAR_005280
I
216
T
HGD_HUMAN
Disease (AKU)
---
A
I
216
T
41
UniProt
VAR_073104
G
217
W
HGD_HUMAN
Disease (AKU)
---
A
G
217
W
42
UniProt
VAR_073105
N
219
S
HGD_HUMAN
Disease (AKU)
---
A
N
219
S
43
UniProt
VAR_005281
R
225
H
HGD_HUMAN
Disease (AKU)
---
A
R
225
H
44
UniProt
VAR_073106
R
225
L
HGD_HUMAN
Disease (AKU)
---
A
R
225
L
45
UniProt
VAR_073107
R
225
P
HGD_HUMAN
Disease (AKU)
---
A
R
225
P
46
UniProt
VAR_005282
F
227
S
HGD_HUMAN
Disease (AKU)
---
A
F
227
S
47
UniProt
VAR_005283
P
230
S
HGD_HUMAN
Disease (AKU)
28942100
A
P
230
S
48
UniProt
VAR_005284
P
230
T
HGD_HUMAN
Disease (AKU)
---
A
P
230
T
49
UniProt
VAR_073108
V
245
F
HGD_HUMAN
Disease (AKU)
---
A
V
245
F
50
UniProt
VAR_073109
Q
258
P
HGD_HUMAN
Disease (AKU)
---
A
Q
258
P
51
UniProt
VAR_073110
H
269
R
HGD_HUMAN
Disease (AKU)
---
A
H
269
R
52
UniProt
VAR_009620
G
270
R
HGD_HUMAN
Disease (AKU)
---
A
G
270
R
53
UniProt
VAR_073111
K
276
N
HGD_HUMAN
Disease (AKU)
---
A
K
276
N
54
UniProt
VAR_005285
D
291
E
HGD_HUMAN
Disease (AKU)
---
A
D
291
E
55
UniProt
VAR_005286
V
300
G
HGD_HUMAN
Disease (AKU)
---
A
V
300
G
56
UniProt
VAR_073112
R
321
P
HGD_HUMAN
Disease (AKU)
---
A
R
321
P
57
UniProt
VAR_073113
F
329
C
HGD_HUMAN
Disease (AKU)
---
A
F
329
C
58
UniProt
VAR_008744
R
330
S
HGD_HUMAN
Disease (AKU)
---
A
R
330
S
59
UniProt
VAR_073114
N
337
D
HGD_HUMAN
Disease (AKU)
---
A
N
337
D
60
UniProt
VAR_073115
P
359
L
HGD_HUMAN
Disease (AKU)
---
A
P
359
L
61
UniProt
VAR_073116
G
360
A
HGD_HUMAN
Disease (AKU)
---
A
G
360
A
62
UniProt
VAR_073117
G
360
R
HGD_HUMAN
Disease (AKU)
---
A
G
360
R
63
UniProt
VAR_073118
G
361
R
HGD_HUMAN
Disease (AKU)
---
A
G
361
R
64
UniProt
VAR_073119
G
362
E
HGD_HUMAN
Disease (AKU)
---
A
G
362
E
65
UniProt
VAR_005287
M
368
V
HGD_HUMAN
Disease (AKU)
120074173
A
M
368
V
66
UniProt
VAR_073120
T
369
N
HGD_HUMAN
Disease (AKU)
---
A
T
369
N
67
UniProt
VAR_008745
H
371
R
HGD_HUMAN
Disease (AKU)
---
A
H
371
R
68
UniProt
VAR_073121
P
373
L
HGD_HUMAN
Disease (AKU)
---
A
P
373
L
69
UniProt
VAR_073122
D
374
H
HGD_HUMAN
Disease (AKU)
---
A
D
374
H
70
UniProt
VAR_073123
E
401
Q
HGD_HUMAN
Disease (AKU)
---
A
E
401
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(14, 14)
Info
All Exons
Exon 1.1a (A:2-5)
Exon 1.3 (A:6-29)
Exon 1.4a (A:30-59)
Exon 1.5a (A:59-94)
Exon 1.6a (A:95-114)
Exon 1.7b (A:115-145)
Exon 1.8 (A:145-157)
Exon 1.9b (A:157-183)
Exon 1.10a (A:184-217)
Exon 1.12 (A:217-258)
Exon 1.13b (A:259-293)
Exon 1.14b (A:294-336)
Exon 1.16a (A:336-396 (gaps))
Exon 1.17b (A:397-440 (gaps))
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.3
03: Boundary 1.3/1.4a
04: Boundary 1.4a/1.5a
05: Boundary 1.5a/1.6a
06: Boundary 1.6a/1.7b
07: Boundary 1.7b/1.8
08: Boundary 1.8/1.9b
09: Boundary 1.9b/1.10a
10: Boundary 1.10a/1.12
11: Boundary 1.12/1.13b
12: Boundary 1.13b/1.14b
13: Boundary 1.14b/1.16a
14: Boundary 1.16a/1.17b
15: Boundary 1.17b/-
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
ENST00000283871
1a
ENSE00001950843
chr3:
120401418-120400944
475
HGD_HUMAN
1-5
5
1
A:2-5
4
1.3
ENST00000283871
3
ENSE00001737886
chr3:
120394710-120394639
72
HGD_HUMAN
6-29
24
1
A:6-29
24
1.4a
ENST00000283871
4a
ENSE00001774025
chr3:
120393836-120393748
89
HGD_HUMAN
30-59
30
1
A:30-59
30
1.5a
ENST00000283871
5a
ENSE00001725712
chr3:
120389379-120389274
106
HGD_HUMAN
59-94
36
1
A:59-94
36
1.6a
ENST00000283871
6a
ENSE00001658207
chr3:
120371498-120371439
60
HGD_HUMAN
95-114
20
1
A:95-114
20
1.7b
ENST00000283871
7b
ENSE00001740085
chr3:
120369712-120369621
92
HGD_HUMAN
115-145
31
1
A:115-145
31
1.8
ENST00000283871
8
ENSE00001686509
chr3:
120366758-120366724
35
HGD_HUMAN
145-157
13
1
A:145-157
13
1.9b
ENST00000283871
9b
ENSE00001596862
chr3:
120365899-120365820
80
HGD_HUMAN
157-183
27
1
A:157-183
27
1.10a
ENST00000283871
10a
ENSE00002142393
chr3:
120365213-120365114
100
HGD_HUMAN
184-217
34
1
A:184-217
34
1.12
ENST00000283871
12
ENSE00001751280
chr3:
120363290-120363166
125
HGD_HUMAN
217-258
42
1
A:217-258
42
1.13b
ENST00000283871
13b
ENSE00001733639
chr3:
120360540-120360436
105
HGD_HUMAN
259-293
35
1
A:259-293
35
1.14b
ENST00000283871
14b
ENSE00001753143
chr3:
120357428-120357302
127
HGD_HUMAN
294-336
43
1
A:294-336
43
1.16a
ENST00000283871
16a
ENSE00001681668
chr3:
120352175-120351994
182
HGD_HUMAN
336-396
61
1
A:336-396 (gaps)
61
1.17b
ENST00000283871
17b
ENSE00001743017
chr3:
120347376-120347020
357
HGD_HUMAN
397-445
49
1
A:397-440 (gaps)
44
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1eyba_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
RmlC-like cupins
(220)
Family
:
Homogentisate dioxygenase
(2)
Protein domain
:
Homogentisate dioxygenase
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1eyba_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (83 KB)
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