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2QD1
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (66 KB)
Biol.Unit 2 (67 KB)
Biol.Unit 3 (67 KB)
Biol.Unit 4 (69 KB)
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(1)
Title
:
2.2 ANGSTROM STRUCTURE OF THE HUMAN FERROCHELATASE VARIANT E343K WITH SUBSTRATE BOUND
Authors
:
A. E. Medlock, T. A. Dailey, T. A. Ross, H. A. Dailey, W. N. Lanzilotta
Date
:
20 Jun 07 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Ferrochelatase, Heme Biosynthesis, Protopophyrin Ix, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. E. Medlock, T. A. Dailey, T. A. Ross, H. A. Dailey, W. N. Lanzilotta
A Pi-Helix Switch Selective For Porphyrin Deprotonation And Product Release In Human Ferrochelatase.
J. Mol. Biol. V. 373 1006 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: CHOLIC ACID (CHDa)
1b: CHOLIC ACID (CHDb)
2a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2b: FE2/S2 (INORGANIC) CLUSTER (FESb)
2c: FE2/S2 (INORGANIC) CLUSTER (FESc)
2d: FE2/S2 (INORGANIC) CLUSTER (FESd)
3a: IMIDAZOLE (IMDa)
4a: PROTOPORPHYRIN IX (PP9a)
4b: PROTOPORPHYRIN IX (PP9b)
4c: PROTOPORPHYRIN IX (PP9c)
4d: PROTOPORPHYRIN IX (PP9d)
4e: PROTOPORPHYRIN IX (PP9e)
4f: PROTOPORPHYRIN IX (PP9f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CHD
2
Ligand/Ion
CHOLIC ACID
2
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
3
IMD
1
Ligand/Ion
IMIDAZOLE
4
PP9
6
Ligand/Ion
PROTOPORPHYRIN IX
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:196 , SER A:402 , CYS A:403 , CYS A:406 , CYS A:411 , HOH A:1043
BINDING SITE FOR RESIDUE FES A 1001
02
AC2
SOFTWARE
CYS B:196 , SER B:402 , CYS B:403 , CYS B:406 , CYS B:411
BINDING SITE FOR RESIDUE FES B 1002
03
AC3
SOFTWARE
CYS C:196 , ARG C:272 , SER C:402 , CYS C:403 , CYS C:406 , CYS C:411
BINDING SITE FOR RESIDUE FES C 1003
04
AC4
SOFTWARE
CYS D:196 , ARG D:272 , SER D:402 , CYS D:403 , CYS D:406 , CYS D:411
BINDING SITE FOR RESIDUE FES D 1004
05
AC5
SOFTWARE
MET A:76 , GLY A:77 , GLY A:78 , PHE A:88 , LEU A:92 , LEU A:98 , ARG A:115 , ILE A:119 , TYR A:123 , SER A:130 , TYR A:191 , SER A:197 , THR A:198 , HIS A:263 , LEU A:265 , TYR A:276 , VAL A:305 , TRP A:310 , HIS A:341 , ILE A:342 , LYS A:343 , HOH A:1097 , HOH A:1115
BINDING SITE FOR RESIDUE PP9 A 701
06
AC6
SOFTWARE
MET B:76 , GLY B:78 , PHE B:88 , LEU B:89 , LEU B:92 , LEU B:98 , MET B:99 , ARG B:115 , ILE B:119 , TYR B:123 , SER B:130 , THR B:198 , HIS B:263 , TYR B:276 , VAL B:305 , ALA B:336 , HIS B:341 , ILE B:342 , LYS B:343 , HOH B:1135 , HOH B:1153
BINDING SITE FOR RESIDUE PP9 B 702
07
AC7
SOFTWARE
ILE C:111 , ARG C:114 , PRO C:307 , MET C:308 , HOH C:1084 , PRO D:102 , PHE D:110 , ARG D:114 , PP9 D:704 , CHD D:801 , HOH D:1136
BINDING SITE FOR RESIDUE PP9 D 703
08
AC8
SOFTWARE
PRO C:102 , LEU C:107 , PHE C:110 , ILE D:111 , ARG D:114 , PRO D:307 , MET D:308 , PP9 D:703 , CHD D:802 , HOH D:1110
BINDING SITE FOR RESIDUE PP9 D 704
09
AC9
SOFTWARE
MET C:76 , GLY C:77 , GLY C:78 , PHE C:88 , PHE C:93 , LEU C:98 , MET C:99 , ARG C:115 , ILE C:119 , TYR C:123 , SER C:130 , TYR C:191 , SER C:197 , THR C:198 , HIS C:263 , ALA C:336 , PHE C:337 , HIS C:341 , ILE C:342 , LYS C:343 , HOH C:1042 , HOH C:1074
BINDING SITE FOR RESIDUE PP9 C 705
10
BC1
SOFTWARE
MET D:76 , GLY D:77 , GLY D:78 , PHE D:88 , LEU D:89 , LEU D:92 , PHE D:93 , LEU D:98 , ARG D:115 , ILE D:119 , TYR D:123 , SER D:130 , TYR D:191 , THR D:198 , HIS D:263 , PRO D:266 , VAL D:305 , TRP D:310 , ALA D:336 , PHE D:337 , HIS D:341 , ILE D:342 , LYS D:343 , HOH D:1064 , HOH D:1090
BINDING SITE FOR RESIDUE PP9 D 706
11
BC2
SOFTWARE
ARG C:115 , PRO C:307 , HOH C:1054 , HOH C:1084 , PP9 D:703 , HOH D:1136
BINDING SITE FOR RESIDUE CHD D 801
12
BC3
SOFTWARE
HOH C:1106 , ARG D:115 , GLY D:306 , PRO D:307 , PP9 D:704
BINDING SITE FOR RESIDUE CHD D 802
13
BC4
SOFTWARE
PRO B:277 , PRO D:277 , SER D:281 , TRP D:301 , HOH D:1160
BINDING SITE FOR RESIDUE IMD D 901
[
close Site info
]
SAPs(SNPs)/Variants
(22, 88)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_030554 (I71K, chain A/B/C/D, )
02: VAR_012028 (R96Q, chain A/B/C/D, )
03: VAR_030555 (Q139L, chain A/B/C/D, )
04: VAR_030556 (S151P, chain A/B/C/D, )
05: VAR_030557 (E178K, chain A/B/C/D, )
06: VAR_030558 (L182R, chain A/B/C/D, )
07: VAR_002384 (I186T, chain A/B/C/D, )
08: VAR_030559 (Y191H, chain A/B/C/D, )
09: VAR_030560 (P192T, chain A/B/C/D, )
10: VAR_030561 (C236Y, chain A/B/C/D, )
11: VAR_030562 (F260L, chain A/B/C/D, )
12: VAR_054629 (S264L, chain A/B/C/D, )
13: VAR_002385 (M267I, chain A/B/C/D, )
14: VAR_030563 (T283I, chain A/B/C/D, )
15: VAR_030564 (M288K, chain A/B/C/D, )
16: VAR_030565 (P334L, chain A/B/C/D, )
17: VAR_030566 (V362G, chain A/B/C/D, )
18: VAR_030567 (K379N, chain A/B/C/D, )
19: VAR_002386 (H386P, chain A/B/C/D, )
20: VAR_030568 (C406S, chain A/B/C/D, )
21: VAR_030569 (C406Y, chain A/B/C/D, )
22: VAR_002387 (F417S, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_030554
I
71
K
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
I
71
K
02
UniProt
VAR_012028
R
96
Q
HEMH_HUMAN
Polymorphism
1041951
A/B/C/D
R
96
Q
03
UniProt
VAR_030555
Q
139
L
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
Q
139
L
04
UniProt
VAR_030556
S
151
P
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
S
151
P
05
UniProt
VAR_030557
E
178
K
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
E
178
K
06
UniProt
VAR_030558
L
182
R
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
L
182
R
07
UniProt
VAR_002384
I
186
T
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
I
186
T
08
UniProt
VAR_030559
Y
191
H
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
Y
191
H
09
UniProt
VAR_030560
P
192
T
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
P
192
T
10
UniProt
VAR_030561
C
236
Y
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
C
236
Y
11
UniProt
VAR_030562
F
260
L
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
F
260
L
12
UniProt
VAR_054629
S
264
L
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
S
264
L
13
UniProt
VAR_002385
M
267
I
HEMH_HUMAN
Disease (EPP)
118204037
A/B/C/D
M
267
I
14
UniProt
VAR_030563
T
283
I
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
T
283
I
15
UniProt
VAR_030564
M
288
K
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
M
288
K
16
UniProt
VAR_030565
P
334
L
HEMH_HUMAN
Disease (EPP)
150146721
A/B/C/D
P
334
L
17
UniProt
VAR_030566
V
362
G
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
V
362
G
18
UniProt
VAR_030567
K
379
N
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
K
379
N
19
UniProt
VAR_002386
H
386
P
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
H
386
P
20
UniProt
VAR_030568
C
406
S
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
C
406
S
21
UniProt
VAR_030569
C
406
Y
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
C
406
Y
22
UniProt
VAR_002387
F
417
S
HEMH_HUMAN
Disease (EPP)
---
A/B/C/D
F
417
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: FERROCHELATASE (A:258-276,B:258-276,C:258-276,D:25...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FERROCHELATASE
PS00534
Ferrochelatase signature.
HEMH_HUMAN
258-276
4
A:258-276
B:258-276
C:258-276
D:258-276
[
close PROSITE info
]
Exons
(10, 40)
Info
All Exons
Exon 1.2a (A:65-65 | B:65-65 | C:65-65 | D:65...)
Exon 1.3 (A:65-105 | B:65-105 | C:65-105 | D...)
Exon 1.4 (A:105-155 | B:105-155 | C:105-155 ...)
Exon 1.5 (A:155-200 | B:155-200 | C:155-200 ...)
Exon 1.6 (A:200-235 | B:200-235 | C:200-235 ...)
Exon 1.7 (A:236-268 | B:236-268 | C:236-268 ...)
Exon 1.8 (A:269-304 | B:269-304 | C:269-304 ...)
Exon 1.9 (A:305-359 | B:305-359 | C:305-359 ...)
Exon 1.10 (A:360-379 | B:360-379 | C:360-379 ...)
Exon 1.11b (A:380-423 | B:380-423 | C:380-423 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2a
02: Boundary 1.2a/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 1.10/1.11b
11: Boundary 1.11b/-
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
ENST00000262093
1a
ENSE00001229850
chr18:
55254004-55253786
219
HEMH_HUMAN
1-23
23
0
-
-
1.2a
ENST00000262093
2a
ENSE00000669631
chr18:
55247431-55247305
127
HEMH_HUMAN
23-65
43
4
A:65-65
B:65-65
C:65-65
D:65-65
1
1
1
1
1.3
ENST00000262093
3
ENSE00001229830
chr18:
55240597-55240478
120
HEMH_HUMAN
65-105
41
4
A:65-105
B:65-105
C:65-105
D:65-105
41
41
41
41
1.4
ENST00000262093
4
ENSE00000669629
chr18:
55238772-55238624
149
HEMH_HUMAN
105-155
51
4
A:105-155
B:105-155
C:105-155
D:105-155
51
51
51
51
1.5
ENST00000262093
5
ENSE00000669628
chr18:
55233813-55233679
135
HEMH_HUMAN
155-200
46
4
A:155-200
B:155-200
C:155-200
D:155-200
46
46
46
46
1.6
ENST00000262093
6
ENSE00000669627
chr18:
55230212-55230106
107
HEMH_HUMAN
200-235
36
4
A:200-235
B:200-235
C:200-235
D:200-235
36
36
36
36
1.7
ENST00000262093
7
ENSE00001229801
chr18:
55226475-55226377
99
HEMH_HUMAN
236-268
33
4
A:236-268
B:236-268
C:236-268
D:236-268
33
33
33
33
1.8
ENST00000262093
8
ENSE00000669625
chr18:
55222184-55222077
108
HEMH_HUMAN
269-304
36
4
A:269-304
B:269-304
C:269-304
D:269-304
36
36
36
36
1.9
ENST00000262093
9
ENSE00001229786
chr18:
55221656-55221492
165
HEMH_HUMAN
305-359
55
4
A:305-359
B:305-359
C:305-359
D:305-359
55
55
55
55
1.10
ENST00000262093
10
ENSE00000669622
chr18:
55218606-55218547
60
HEMH_HUMAN
360-379
20
4
A:360-379
B:360-379
C:360-379
D:360-379
20
20
20
20
1.11b
ENST00000262093
11b
ENSE00001229844
chr18:
55218078-55215515
2564
HEMH_HUMAN
380-423
44
4
A:380-423
B:380-423
C:380-423
D:380-423
44
44
44
44
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2qd1a_ (A:)
1b: SCOP_d2qd1b_ (B:)
1c: SCOP_d2qd1c_ (C:)
1d: SCOP_d2qd1d_ (D:)
View:
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Classes
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)
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)
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(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Chelatase-like
(149)
Superfamily
:
Chelatase
(46)
Family
:
Ferrochelatase
(37)
Protein domain
:
Ferrochelatase
(34)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d2qd1a_
A:
1b
d2qd1b_
B:
1c
d2qd1c_
C:
1d
d2qd1d_
D:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2qd1A02 (A:228-370)
1b: CATH_2qd1B02 (B:228-370)
1c: CATH_2qd1C02 (C:228-370)
1d: CATH_2qd1D02 (D:228-370)
1e: CATH_2qd1A01 (A:65-227,A:371-423)
1f: CATH_2qd1B01 (B:65-227,B:371-423)
1g: CATH_2qd1C01 (C:65-227,C:371-423)
1h: CATH_2qd1D01 (D:65-227,D:371-423)
View:
Select:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1400, no name defined]
(36)
Human (Homo sapiens)
(15)
1a
2qd1A02
A:228-370
1b
2qd1B02
B:228-370
1c
2qd1C02
C:228-370
1d
2qd1D02
D:228-370
1e
2qd1A01
A:65-227,A:371-423
1f
2qd1B01
B:65-227,B:371-423
1g
2qd1C01
C:65-227,C:371-423
1h
2qd1D01
D:65-227,D:371-423
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Ferrochelatase_2qd1D01 (D:68-389)
1b: PFAM_Ferrochelatase_2qd1D02 (D:68-389)
1c: PFAM_Ferrochelatase_2qd1D03 (D:68-389)
1d: PFAM_Ferrochelatase_2qd1D04 (D:68-389)
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Chelatase
(20)
Family
:
Ferrochelatase
(12)
Homo sapiens (Human)
(6)
1a
Ferrochelatase-2qd1D01
D:68-389
1b
Ferrochelatase-2qd1D02
D:68-389
1c
Ferrochelatase-2qd1D03
D:68-389
1d
Ferrochelatase-2qd1D04
D:68-389
[
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
Chain B
Chain C
Chain D
Asymmetric Unit 1
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(selected part)
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(e.g.: "#3cb371" or "60,179,113")
Stereo
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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)
[
close Script example commands
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Log
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") .
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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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