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2QD1
Biol. Unit 3
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
(2, 2)
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
-1
Ligand/Ion
CHOLIC ACID
2
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
3
IMD
-1
Ligand/Ion
IMIDAZOLE
4
PP9
1
Ligand/Ion
PROTOPORPHYRIN IX
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
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
2
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
3
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
4
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
5
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
6
BC3
SOFTWARE
HOH C:1106 , ARG D:115 , GLY D:306 , PRO D:307 , PP9 D:704
BINDING SITE FOR RESIDUE CHD D 802
[
close Site info
]
SAPs(SNPs)/Variants
(22, 22)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_030554 (I71K, chain C, )
02: VAR_012028 (R96Q, chain C, )
03: VAR_030555 (Q139L, chain C, )
04: VAR_030556 (S151P, chain C, )
05: VAR_030557 (E178K, chain C, )
06: VAR_030558 (L182R, chain C, )
07: VAR_002384 (I186T, chain C, )
08: VAR_030559 (Y191H, chain C, )
09: VAR_030560 (P192T, chain C, )
10: VAR_030561 (C236Y, chain C, )
11: VAR_030562 (F260L, chain C, )
12: VAR_054629 (S264L, chain C, )
13: VAR_002385 (M267I, chain C, )
14: VAR_030563 (T283I, chain C, )
15: VAR_030564 (M288K, chain C, )
16: VAR_030565 (P334L, chain C, )
17: VAR_030566 (V362G, chain C, )
18: VAR_030567 (K379N, chain C, )
19: VAR_002386 (H386P, chain C, )
20: VAR_030568 (C406S, chain C, )
21: VAR_030569 (C406Y, chain C, )
22: VAR_002387 (F417S, chain C, )
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)
---
C
I
71
K
02
UniProt
VAR_012028
R
96
Q
HEMH_HUMAN
Polymorphism
1041951
C
R
96
Q
03
UniProt
VAR_030555
Q
139
L
HEMH_HUMAN
Disease (EPP)
---
C
Q
139
L
04
UniProt
VAR_030556
S
151
P
HEMH_HUMAN
Disease (EPP)
---
C
S
151
P
05
UniProt
VAR_030557
E
178
K
HEMH_HUMAN
Disease (EPP)
---
C
E
178
K
06
UniProt
VAR_030558
L
182
R
HEMH_HUMAN
Disease (EPP)
---
C
L
182
R
07
UniProt
VAR_002384
I
186
T
HEMH_HUMAN
Disease (EPP)
---
C
I
186
T
08
UniProt
VAR_030559
Y
191
H
HEMH_HUMAN
Disease (EPP)
---
C
Y
191
H
09
UniProt
VAR_030560
P
192
T
HEMH_HUMAN
Disease (EPP)
---
C
P
192
T
10
UniProt
VAR_030561
C
236
Y
HEMH_HUMAN
Disease (EPP)
---
C
C
236
Y
11
UniProt
VAR_030562
F
260
L
HEMH_HUMAN
Disease (EPP)
---
C
F
260
L
12
UniProt
VAR_054629
S
264
L
HEMH_HUMAN
Disease (EPP)
---
C
S
264
L
13
UniProt
VAR_002385
M
267
I
HEMH_HUMAN
Disease (EPP)
118204037
C
M
267
I
14
UniProt
VAR_030563
T
283
I
HEMH_HUMAN
Disease (EPP)
---
C
T
283
I
15
UniProt
VAR_030564
M
288
K
HEMH_HUMAN
Disease (EPP)
---
C
M
288
K
16
UniProt
VAR_030565
P
334
L
HEMH_HUMAN
Disease (EPP)
150146721
C
P
334
L
17
UniProt
VAR_030566
V
362
G
HEMH_HUMAN
Disease (EPP)
---
C
V
362
G
18
UniProt
VAR_030567
K
379
N
HEMH_HUMAN
Disease (EPP)
---
C
K
379
N
19
UniProt
VAR_002386
H
386
P
HEMH_HUMAN
Disease (EPP)
---
C
H
386
P
20
UniProt
VAR_030568
C
406
S
HEMH_HUMAN
Disease (EPP)
---
C
C
406
S
21
UniProt
VAR_030569
C
406
Y
HEMH_HUMAN
Disease (EPP)
---
C
C
406
Y
22
UniProt
VAR_002387
F
417
S
HEMH_HUMAN
Disease (EPP)
---
C
F
417
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: FERROCHELATASE (C: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
1
-
-
C: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_d2qd1a_ (A:)
1b: SCOP_d2qd1b_ (B:)
1c: SCOP_d2qd1c_ (C:)
1d: SCOP_d2qd1d_ (D:)
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)
(
)
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(
)
(
)
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:
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
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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Select:
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
[
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]
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Asymmetric Unit 1
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