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2QMI
Asym. Unit
Info
Asym.Unit (622 KB)
Biol.Unit 1 (615 KB)
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(1)
Title
:
STRUCTURE OF THE OCTAMERIC PENICILLIN-BINDING PROTEIN HOMOLOGUE FROM PYROCOCCUS ABYSSI
Authors
:
V. Delfosse, E. Girard, L. Moulinier, P. Schultz, C. Mayer
Date
:
16 Jul 07 (Deposition) - 22 Jul 08 (Release) - 16 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Pab87, Octamer, Lu-Hpdo3A, Pbp, Archaea, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Delfosse, E. Girard, C. Birck, M. Delmarcelle, M. Delarue, O. Poch, P. Schultz, C. Mayer
Structure Of The Archaeal Pab87 Peptidase Reveals A Novel Self-Compartmentalizing Protease Family
Plos One V. 4 E4712 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 21)
Info
All Hetero Components
1a: 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10... (DO3a)
1b: 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10... (DO3b)
1c: 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10... (DO3c)
1d: 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10... (DO3d)
2a: LUTETIUM (III) ION (LUa)
2b: LUTETIUM (III) ION (LUb)
2c: LUTETIUM (III) ION (LUc)
2d: LUTETIUM (III) ION (LUd)
2e: LUTETIUM (III) ION (LUe)
2f: LUTETIUM (III) ION (LUf)
2g: LUTETIUM (III) ION (LUg)
2h: LUTETIUM (III) ION (LUh)
2i: LUTETIUM (III) ION (LUi)
2j: LUTETIUM (III) ION (LUj)
2k: LUTETIUM (III) ION (LUk)
2l: LUTETIUM (III) ION (LUl)
2m: LUTETIUM (III) ION (LUm)
2n: LUTETIUM (III) ION (LUn)
2o: LUTETIUM (III) ION (LUo)
2p: LUTETIUM (III) ION (LUp)
2q: LUTETIUM (III) ION (LUq)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DO3
4
Ligand/Ion
10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID
2
LU
17
Ligand/Ion
LUTETIUM (III) ION
[
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Sites
(14, 14)
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)
14: BC5 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:509 , HOH A:531 , HOH A:694 , HOH A:695 , HOH A:697 , HOH A:730
BINDING SITE FOR RESIDUE LU A 448
02
AC2
SOFTWARE
HOH B:708 , HOH B:709 , HOH B:712
BINDING SITE FOR RESIDUE LU B 448
03
AC3
SOFTWARE
HOH C:661 , HOH C:662 , HOH C:663 , HOH C:678 , HOH C:686
BINDING SITE FOR RESIDUE LU C 448
04
AC4
SOFTWARE
HOH G:800
BINDING SITE FOR RESIDUE LU G 448
05
AC5
SOFTWARE
HOH F:555 , HOH F:556 , HOH F:756 , HOH F:757 , HOH F:759 , HOH F:760
BINDING SITE FOR RESIDUE LU F 449
06
AC6
SOFTWARE
HOH B:703 , HOH B:705
BINDING SITE FOR RESIDUE LU B 449
07
AC7
SOFTWARE
HOH C:672 , HOH C:673 , HOH C:674 , HOH F:560
BINDING SITE FOR RESIDUE LU C 449
08
AC8
SOFTWARE
HOH D:657 , HOH D:659
BINDING SITE FOR RESIDUE LU D 449
09
AC9
SOFTWARE
HOH E:777 , HOH E:778
BINDING SITE FOR RESIDUE LU E 449
10
BC1
SOFTWARE
HOH G:528 , HOH H:518 , HOH H:724
BINDING SITE FOR RESIDUE LU G 450
11
BC2
SOFTWARE
ASP E:81 , HIS E:102 , HOH E:745 , HOH E:747 , GLU H:297 , GLU H:318 , LYS H:319 , HOH H:638
BINDING SITE FOR RESIDUE DO3 E 450
12
BC3
SOFTWARE
GLU F:297 , GLU F:318 , LYS F:319 , HOH F:702 , ASP G:81 , HIS G:102 , HOH G:706 , HOH G:800
BINDING SITE FOR RESIDUE DO3 G 451
13
BC4
SOFTWARE
ASP H:81 , HIS H:102 , TYR H:286
BINDING SITE FOR RESIDUE DO3 H 449
14
BC5
SOFTWARE
ASP F:81 , HIS F:102 , HOH F:529
BINDING SITE FOR RESIDUE DO3 F 451
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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;
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Exons
(0, 0)
Info
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_Beta_lactamase_2qmiH01 (H:6-348)
1b: PFAM_Beta_lactamase_2qmiH02 (H:6-348)
1c: PFAM_Beta_lactamase_2qmiH03 (H:6-348)
1d: PFAM_Beta_lactamase_2qmiH04 (H:6-348)
1e: PFAM_Beta_lactamase_2qmiH05 (H:6-348)
1f: PFAM_Beta_lactamase_2qmiH06 (H:6-348)
1g: PFAM_Beta_lactamase_2qmiH07 (H:6-348)
1h: PFAM_Beta_lactamase_2qmiH08 (H:6-348)
2a: PFAM_Pab87_oct_2qmiH09 (H:350-446)
2b: PFAM_Pab87_oct_2qmiH10 (H:350-446)
2c: PFAM_Pab87_oct_2qmiH11 (H:350-446)
2d: PFAM_Pab87_oct_2qmiH12 (H:350-446)
2e: PFAM_Pab87_oct_2qmiH13 (H:350-446)
2f: PFAM_Pab87_oct_2qmiH14 (H:350-446)
2g: PFAM_Pab87_oct_2qmiH15 (H:350-446)
2h: PFAM_Pab87_oct_2qmiH16 (H:350-446)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta-lactamase
(210)
Family
:
Beta-lactamase
(79)
Pyrococcus abyssi (strain GE5 / Orsay)
(1)
1a
Beta-lactamase-2qmiH01
H:6-348
1b
Beta-lactamase-2qmiH02
H:6-348
1c
Beta-lactamase-2qmiH03
H:6-348
1d
Beta-lactamase-2qmiH04
H:6-348
1e
Beta-lactamase-2qmiH05
H:6-348
1f
Beta-lactamase-2qmiH06
H:6-348
1g
Beta-lactamase-2qmiH07
H:6-348
1h
Beta-lactamase-2qmiH08
H:6-348
Clan
:
no clan defined [family: Pab87_oct]
(1)
Family
:
Pab87_oct
(1)
Pyrococcus abyssi (strain GE5 / Orsay)
(1)
2a
Pab87_oct-2qmiH09
H:350-446
2b
Pab87_oct-2qmiH10
H:350-446
2c
Pab87_oct-2qmiH11
H:350-446
2d
Pab87_oct-2qmiH12
H:350-446
2e
Pab87_oct-2qmiH13
H:350-446
2f
Pab87_oct-2qmiH14
H:350-446
2g
Pab87_oct-2qmiH15
H:350-446
2h
Pab87_oct-2qmiH16
H:350-446
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Asym.Unit (622 KB)
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