PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2HRE
Biol. Unit 1
Info
Asym.Unit (255 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (125 KB)
Biol.Unit 3 (246 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF HUMAN FERROCHELATASE VARIANT E343K WITH PROTOPORPHYRIN IX BOUND
Authors
:
A. Medlock, L. Swartz, T. A. Dailey, H. A. Dailey, W. N. Lanzilotta
Date
:
20 Jul 06 (Deposition) - 13 Mar 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Heme Synthesis, Ferrochelatase, Protoporphyrin Ix, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Medlock, L. Swartz, T. A. Dailey, H. A. Dailey, W. N. Lanzilotta
Substrate Interactions With Human Ferrochelatase
Proc. Natl. Acad. Sci. Usa V. 104 1789 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 6)
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: PROTOPORPHYRIN IX (PP9a)
3b: PROTOPORPHYRIN IX (PP9b)
3c: PROTOPORPHYRIN IX (PP9c)
3d: PROTOPORPHYRIN IX (PP9d)
3e: PROTOPORPHYRIN IX (PP9e)
3f: PROTOPORPHYRIN IX (PP9f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CHD
1
Ligand/Ion
CHOLIC ACID
2
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
3
PP9
3
Ligand/Ion
PROTOPORPHYRIN IX
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC9 (SOFTWARE)
7: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET A:76 , GLY A:77 , GLY A:78 , PHE A:88 , LEU A:89 , LEU A:92 , LEU A:98 , MET A:99 , ARG A:115 , ILE A:119 , TYR A:123 , SER A:130 , TYR A:191 , SER A:197 , THR A:198 , HIS A:263 , PRO A:266 , TYR A:276 , VAL A:305 , TRP A:310 , ALA A:336 , HIS A:341 , ILE A:342 , LYS A:343
BINDING SITE FOR RESIDUE PP9 A 601
2
AC2
SOFTWARE
MET B:76 , GLY B:77 , GLY B:78 , LEU B:92 , LEU B:98 , MET B:99 , ARG B:115 , ILE B:119 , TYR B:123 , SER B:130 , ILE B:132 , TYR B:191 , THR B:198 , HIS B:263 , PRO B:266 , TYR B:276 , TRP B:310 , ALA B:336 , HIS B:341 , ILE B:342 , LYS B:343 , HOH B:725 , HOH B:727
BINDING SITE FOR RESIDUE PP9 B 602
3
AC3
SOFTWARE
ILE B:111 , PRO B:307 , MET B:308 , CHD B:701 , HOH B:766 , PRO D:102 , PHE D:110 , ARG D:114 , PP9 D:604
BINDING SITE FOR RESIDUE PP9 B 603
4
AC4
SOFTWARE
PHE B:110 , ARG B:114 , PP9 B:603 , ILE D:111 , PRO D:307 , MET D:308 , CHD D:702 , HOH D:727 , HOH D:728 , HOH D:729
BINDING SITE FOR RESIDUE PP9 D 604
5
AC7
SOFTWARE
LYS B:118 , PRO B:307 , PP9 B:603 , HOH D:719
BINDING SITE FOR RESIDUE CHD B 701
6
AC9
SOFTWARE
CYS A:196 , SER A:402 , CYS A:403 , CYS A:406 , CYS A:411
BINDING SITE FOR RESIDUE FES A 501
7
BC1
SOFTWARE
CYS B:196 , ARG B:272 , SER B:402 , CYS B:403 , CYS B:406 , CYS B:411
BINDING SITE FOR RESIDUE FES B 502
[
close Site info
]
SAPs(SNPs)/Variants
(22, 44)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_030554 (I71K, chain A/B, )
02: VAR_012028 (R96Q, chain A/B, )
03: VAR_030555 (Q139L, chain A/B, )
04: VAR_030556 (S151P, chain A/B, )
05: VAR_030557 (E178K, chain A/B, )
06: VAR_030558 (L182R, chain A/B, )
07: VAR_002384 (I186T, chain A/B, )
08: VAR_030559 (Y191H, chain A/B, )
09: VAR_030560 (P192T, chain A/B, )
10: VAR_030561 (C236Y, chain A/B, )
11: VAR_030562 (F260L, chain A/B, )
12: VAR_054629 (S264L, chain A/B, )
13: VAR_002385 (M267I, chain A/B, )
14: VAR_030563 (T283I, chain A/B, )
15: VAR_030564 (M288K, chain A/B, )
16: VAR_030565 (P334L, chain A/B, )
17: VAR_030566 (V362G, chain A/B, )
18: VAR_030567 (K379N, chain A/B, )
19: VAR_002386 (H386P, chain A/B, )
20: VAR_030568 (C406S, chain A/B, )
21: VAR_030569 (C406Y, chain A/B, )
22: VAR_002387 (F417S, chain A/B, )
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
I
71
K
02
UniProt
VAR_012028
R
96
Q
HEMH_HUMAN
Polymorphism
1041951
A/B
R
96
Q
03
UniProt
VAR_030555
Q
139
L
HEMH_HUMAN
Disease (EPP)
---
A/B
Q
139
L
04
UniProt
VAR_030556
S
151
P
HEMH_HUMAN
Disease (EPP)
---
A/B
S
151
P
05
UniProt
VAR_030557
E
178
K
HEMH_HUMAN
Disease (EPP)
---
A/B
E
178
K
06
UniProt
VAR_030558
L
182
R
HEMH_HUMAN
Disease (EPP)
---
A/B
L
182
R
07
UniProt
VAR_002384
I
186
T
HEMH_HUMAN
Disease (EPP)
---
A/B
I
186
T
08
UniProt
VAR_030559
Y
191
H
HEMH_HUMAN
Disease (EPP)
---
A/B
Y
191
H
09
UniProt
VAR_030560
P
192
T
HEMH_HUMAN
Disease (EPP)
---
A/B
P
192
T
10
UniProt
VAR_030561
C
236
Y
HEMH_HUMAN
Disease (EPP)
---
A/B
C
236
Y
11
UniProt
VAR_030562
F
260
L
HEMH_HUMAN
Disease (EPP)
---
A/B
F
260
L
12
UniProt
VAR_054629
S
264
L
HEMH_HUMAN
Disease (EPP)
---
A/B
S
264
L
13
UniProt
VAR_002385
M
267
I
HEMH_HUMAN
Disease (EPP)
118204037
A/B
M
267
I
14
UniProt
VAR_030563
T
283
I
HEMH_HUMAN
Disease (EPP)
---
A/B
T
283
I
15
UniProt
VAR_030564
M
288
K
HEMH_HUMAN
Disease (EPP)
---
A/B
M
288
K
16
UniProt
VAR_030565
P
334
L
HEMH_HUMAN
Disease (EPP)
150146721
A/B
P
334
L
17
UniProt
VAR_030566
V
362
G
HEMH_HUMAN
Disease (EPP)
---
A/B
V
362
G
18
UniProt
VAR_030567
K
379
N
HEMH_HUMAN
Disease (EPP)
---
A/B
K
379
N
19
UniProt
VAR_002386
H
386
P
HEMH_HUMAN
Disease (EPP)
---
A/B
H
386
P
20
UniProt
VAR_030568
C
406
S
HEMH_HUMAN
Disease (EPP)
---
A/B
C
406
S
21
UniProt
VAR_030569
C
406
Y
HEMH_HUMAN
Disease (EPP)
---
A/B
C
406
Y
22
UniProt
VAR_002387
F
417
S
HEMH_HUMAN
Disease (EPP)
---
A/B
F
417
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: FERROCHELATASE (A:258-276,B:258-276)
;
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
2
A:258-276
B:258-276
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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, 4)
Info
All SCOP Domains
1a: SCOP_d2hrea_ (A:)
1b: SCOP_d2hreb_ (B:)
1c: SCOP_d2hrec_ (C:)
1d: SCOP_d2hred_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
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
d2hrea_
A:
1b
d2hreb_
B:
1c
d2hrec_
C:
1d
d2hred_
D:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2hreA02 (A:228-370)
1b: CATH_2hreB02 (B:228-370)
1c: CATH_2hreC02 (C:228-370)
1d: CATH_2hreD02 (D:228-370)
1e: CATH_2hreA01 (A:65-227,A:371-423)
1f: CATH_2hreB01 (B:65-227,B:371-423)
1g: CATH_2hreC01 (C:65-227,C:371-423)
1h: CATH_2hreD01 (D:65-227,D:371-423)
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
:
[code=3.40.50.1400, no name defined]
(36)
Human (Homo sapiens)
(15)
1a
2hreA02
A:228-370
1b
2hreB02
B:228-370
1c
2hreC02
C:228-370
1d
2hreD02
D:228-370
1e
2hreA01
A:65-227,A:371-423
1f
2hreB01
B:65-227,B:371-423
1g
2hreC01
C:65-227,C:371-423
1h
2hreD01
D:65-227,D:371-423
[
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
Chain B
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
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
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
]
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") .
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (255 KB)
Header - Asym.Unit
Biol.Unit 1 (126 KB)
Header - Biol.Unit 1
Biol.Unit 2 (125 KB)
Header - Biol.Unit 2
Biol.Unit 3 (246 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2HRE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help