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2QD2
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (131 KB)
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(1)
Title
:
F110A VARIANT OF HUMAN FERROCHELATASE WITH PROTOHEME BOUND
Authors
:
A. E. Medlock, T. A. Dailey, T. A. Ross, H. A. Dailey, W. N. Lanzilota
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
Biol. Unit 1: A,B (1x)
Keywords
:
Heme Synthesis, Ferrochelatase, Protoporphyrin Ix, Heme Biosynthesis, Iron, Lyase, Porphyrin Biosynthesis, Biosynthetic Protein
(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
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Hetero Components
(5, 13)
Info
All Hetero Components
1a: BICARBONATE ION (BCTa)
1b: BICARBONATE ION (BCTb)
2a: CHOLIC ACID (CHDa)
2b: CHOLIC ACID (CHDb)
2c: CHOLIC ACID (CHDc)
2d: CHOLIC ACID (CHDd)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5a: IMIDAZOLE (IMDa)
5b: IMIDAZOLE (IMDb)
5c: IMIDAZOLE (IMDc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCT
2
Ligand/Ion
BICARBONATE ION
2
CHD
4
Ligand/Ion
CHOLIC ACID
3
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
IMD
3
Ligand/Ion
IMIDAZOLE
[
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
MET A:76 , LEU A:98 , TYR A:165 , SER A:197 , HEM A:602 , HOH A:646
BINDING SITE FOR RESIDUE BCT A 1
02
AC2
SOFTWARE
MET B:76 , LEU B:98 , TYR B:165 , TYR B:191 , SER B:197 , THR B:198 , HEM B:601 , HOH B:636
BINDING SITE FOR RESIDUE BCT B 2
03
AC3
SOFTWARE
CYS A:196 , SER A:402 , CYS A:403 , CYS A:406 , CYS A:411
BINDING SITE FOR RESIDUE FES A 424
04
AC4
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 424
05
AC5
SOFTWARE
SER A:264 , GLN A:302 , SER A:303 , HEM A:602
BINDING SITE FOR RESIDUE IMD A 425
06
AC6
SOFTWARE
SER B:264 , GLN B:302 , SER B:303 , TRP B:310 , HEM B:601
BINDING SITE FOR RESIDUE IMD B 425
07
AC7
SOFTWARE
PRO A:277 , HOH A:738 , HOH A:755 , PRO B:277 , SER B:281
BINDING SITE FOR RESIDUE IMD A 3
08
AC8
SOFTWARE
CHD B:4 , MET B:99 , LEU B:101 , ARG B:115 , LYS B:118 , PRO B:266 , VAL B:305 , GLY B:306 , MET B:308 , HEM B:601 , HOH B:632 , HOH B:737
BINDING SITE FOR RESIDUE CHD B 1
09
AC9
SOFTWARE
MET A:99 , THR A:100 , LEU A:101 , ARG A:114 , ARG A:115 , PRO A:266 , SER A:268 , VAL A:305 , CHD A:426 , HEM A:602
BINDING SITE FOR RESIDUE CHD A 2
10
BC1
SOFTWARE
CHD A:2 , LEU A:101 , ARG A:114 , HOH A:748 , LEU B:107 , ALA B:110
BINDING SITE FOR RESIDUE CHD A 426
11
BC2
SOFTWARE
LYS A:106 , ALA A:110 , CHD B:1 , LEU B:101
BINDING SITE FOR RESIDUE CHD B 4
12
BC3
SOFTWARE
BCT A:1 , CHD A:2 , MET A:76 , PHE A:93 , LEU A:98 , ARG A:115 , ILE A:119 , TYR A:191 , SER A:197 , THR A:198 , HIS A:263 , LEU A:265 , PRO A:266 , TYR A:276 , VAL A:305 , ALA A:336 , PHE A:337 , HIS A:341 , ILE A:342 , IMD A:425 , HOH A:623 , HOH A:691 , HOH A:754
BINDING SITE FOR RESIDUE HEM A 602
13
BC4
SOFTWARE
CHD B:1 , BCT B:2 , MET B:76 , PHE B:93 , ARG B:115 , TYR B:191 , SER B:197 , HIS B:263 , LEU B:265 , PRO B:266 , VAL B:305 , TRP B:310 , ALA B:336 , HIS B:341 , ILE B:342 , IMD B:425 , HOH B:674
BINDING SITE FOR RESIDUE HEM B 601
[
close Site info
]
SAPs(SNPs)/Variants
(22, 44)
Info
(mutated residues are not available)
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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2qd2a_ (A:)
1b: SCOP_d2qd2b_ (B:)
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
:
automated matches
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2qd2a_
A:
1b
d2qd2b_
B:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2qd2A02 (A:228-370)
1b: CATH_2qd2B02 (B:228-370)
1c: CATH_2qd2A01 (A:65-227,A:371-423)
1d: CATH_2qd2B01 (B:65-227,B: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
2qd2A02
A:228-370
1b
2qd2B02
B:228-370
1c
2qd2A01
A:65-227,A:371-423
1d
2qd2B01
B:65-227,B:371-423
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Ferrochelatase_2qd2B01 (B:68-389)
1b: PFAM_Ferrochelatase_2qd2B02 (B:68-389)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Chelatase
(20)
Family
:
Ferrochelatase
(12)
Homo sapiens (Human)
(6)
1a
Ferrochelatase-2qd2B01
B:68-389
1b
Ferrochelatase-2qd2B02
B:68-389
[
close Pfam info
]
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