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3Q2K
Biol. Unit 1
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Asym.Unit (909 KB)
Biol.Unit 1 (453 KB)
Biol.Unit 2 (449 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE WLBA DEHYDROGENASE FROM BORDETELLA PERTUSSIS IN COMPLEX WITH NADH AND UDP-GLCNACA
Authors
:
H. M. Holden, J. B. Thoden
Date
:
20 Dec 10 (Deposition) - 19 Jan 11 (Release) - 17 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.13
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Biol. Unit 2: I,J,K,L,M,N,O,P (1x)
Keywords
:
Rossmann Fold, Dehydrogenase, Nad, Udp-Sugar, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. B. Thoden, H. M. Holden
Biochemical And Structural Characterization Of Wlba From Bordetella Pertussis And Chromobacterium Violaceum: Enzymes Required For The Biosynthesis Of 2, 3-Diacetamido-2, 3-Dideoxy-D-Mannuronic Acid.
Biochemistry V. 50 1483 2011
[
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Hetero Components
(2, 16)
Info
All Hetero Components
1a: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7a)
1b: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7b)
1c: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7c)
1d: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7d)
1e: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7e)
1f: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7f)
1g: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7g)
1h: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7h)
1i: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7i)
1j: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7j)
1k: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7k)
1l: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7l)
1m: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7m)
1n: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7n)
1o: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7o)
1p: (2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[... (HP7p)
2a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
2b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
2c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
2d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
2e: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIe)
2f: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIf)
2g: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIg)
2h: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIh)
2i: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIi)
2j: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIj)
2k: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIk)
2l: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIl)
2m: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIm)
2n: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIn)
2o: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIo)
2p: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HP7
8
Ligand/Ion
(2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[(2R,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-3,4-DIHYDROXY-OXANE-2-CARBOXYLIC ACID
2
NAI
8
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(18, 18)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: CC8 (SOFTWARE)
18: DC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:17 , CYS A:18 , GLY A:19 , ARG A:20 , ILE A:21 , ASP A:43 , ASN A:45 , ALA A:79 , THR A:80 , PRO A:81 , SER A:82 , LEU A:84 , HIS A:85 , GLN A:88 , GLU A:102 , LYS A:103 , GLN A:131 , TRP A:174 , ARG A:175 , HIS A:191 , HIS A:301 , HOH A:351 , HOH A:353 , HP7 A:550
BINDING SITE FOR RESIDUE NAI A 500
02
AC2
SOFTWARE
ARG A:20 , LYS A:103 , GLN A:131 , TRP A:162 , THR A:163 , ARG A:164 , PRO A:165 , TYR A:168 , ASN A:187 , GLN A:188 , HIS A:191 , GLN A:246 , ASN A:247 , HOH A:353 , HOH A:367 , HOH A:376 , HOH A:377 , NAI A:500 , GLU O:278 , PRO O:279
BINDING SITE FOR RESIDUE HP7 A 550
03
AC3
SOFTWARE
GLY B:17 , GLY B:19 , ARG B:20 , ILE B:21 , ASP B:43 , THR B:44 , ASN B:45 , ALA B:79 , THR B:80 , SER B:82 , LEU B:84 , HIS B:85 , GLN B:88 , GLU B:102 , LYS B:103 , GLN B:131 , TRP B:174 , ARG B:175 , HIS B:191 , HP7 B:550
BINDING SITE FOR RESIDUE NAI B 500
04
AC4
SOFTWARE
LYS B:103 , TRP B:162 , THR B:163 , ARG B:164 , PRO B:165 , TYR B:168 , ASN B:187 , GLN B:188 , HIS B:191 , GLN B:246 , ASN B:247 , HOH B:358 , HOH B:365 , NAI B:500
BINDING SITE FOR RESIDUE HP7 B 550
05
AC5
SOFTWARE
GLY C:17 , CYS C:18 , GLY C:19 , ARG C:20 , ILE C:21 , ASP C:43 , THR C:44 , ASN C:45 , ALA C:79 , THR C:80 , SER C:82 , HIS C:85 , GLN C:88 , GLU C:102 , LYS C:103 , GLN C:131 , TRP C:174 , ARG C:175 , HIS C:301 , HOH C:356 , HP7 C:550
BINDING SITE FOR RESIDUE NAI C 500
06
AC6
SOFTWARE
ARG C:20 , LYS C:103 , GLN C:131 , ASN C:132 , TRP C:162 , THR C:163 , ARG C:164 , PRO C:165 , TYR C:168 , ASN C:187 , GLN C:188 , HIS C:191 , GLN C:246 , ASN C:247 , HOH C:370 , NAI C:500 , ARG N:287
BINDING SITE FOR RESIDUE HP7 C 550
07
AC7
SOFTWARE
GLY D:17 , GLY D:19 , ARG D:20 , ILE D:21 , ASP D:43 , THR D:44 , ASN D:45 , THR D:80 , PRO D:81 , SER D:82 , LEU D:84 , HIS D:85 , GLN D:88 , GLU D:102 , LYS D:103 , GLN D:131 , TRP D:174 , ARG D:175 , HIS D:191 , HIS D:301 , HP7 D:550
BINDING SITE FOR RESIDUE NAI D 500
08
AC8
SOFTWARE
ARG D:20 , LYS D:103 , TRP D:162 , THR D:163 , ARG D:164 , PRO D:165 , TYR D:168 , ASN D:187 , GLN D:188 , HIS D:191 , GLN D:246 , ASN D:247 , NAI D:500
BINDING SITE FOR RESIDUE HP7 D 550
09
AC9
SOFTWARE
CYS E:18 , GLY E:19 , ARG E:20 , ILE E:21 , ASP E:43 , THR E:44 , ASN E:45 , THR E:80 , SER E:82 , HIS E:85 , GLN E:88 , GLU E:102 , LYS E:103 , GLN E:131 , TRP E:174 , ARG E:175 , HIS E:191 , HP7 E:550
BINDING SITE FOR RESIDUE NAI E 500
10
BC1
SOFTWARE
ARG E:20 , LYS E:103 , ASN E:132 , TRP E:162 , THR E:163 , ARG E:164 , PRO E:165 , TYR E:168 , ASN E:187 , GLN E:188 , HIS E:191 , GLN E:246 , ASN E:247 , NAI E:500
BINDING SITE FOR RESIDUE HP7 E 550
11
BC2
SOFTWARE
CYS F:18 , GLY F:19 , ARG F:20 , ILE F:21 , ASP F:43 , THR F:44 , ASN F:45 , ALA F:79 , THR F:80 , PRO F:81 , SER F:82 , LEU F:84 , HIS F:85 , GLN F:88 , GLU F:102 , LYS F:103 , GLN F:131 , TRP F:174 , ARG F:175 , HIS F:191 , HOH F:358 , HP7 F:550
BINDING SITE FOR RESIDUE NAI F 500
12
BC3
SOFTWARE
ARG F:20 , LYS F:103 , TRP F:162 , THR F:163 , ARG F:164 , PRO F:165 , TYR F:168 , ASN F:187 , GLN F:188 , HIS F:191 , GLN F:246 , ASN F:247 , NAI F:500
BINDING SITE FOR RESIDUE HP7 F 550
13
BC4
SOFTWARE
GLY G:19 , ARG G:20 , ILE G:21 , ASP G:43 , THR G:44 , ASN G:45 , ALA G:79 , THR G:80 , SER G:82 , LEU G:84 , HIS G:85 , GLN G:88 , GLU G:102 , LYS G:103 , GLN G:131 , TRP G:174 , ARG G:175 , HIS G:191 , HOH G:372 , HOH G:373 , HOH G:394 , HP7 G:550
BINDING SITE FOR RESIDUE NAI G 500
14
BC5
SOFTWARE
ARG G:20 , LYS G:103 , GLN G:131 , TRP G:162 , THR G:163 , ARG G:164 , PRO G:165 , TYR G:168 , ASN G:187 , GLN G:188 , HIS G:191 , GLN G:246 , ASN G:247 , HOH G:373 , HOH G:374 , HOH G:380 , HOH G:381 , NAI G:500 , HOH G:537
BINDING SITE FOR RESIDUE HP7 G 550
15
BC6
SOFTWARE
CYS H:18 , GLY H:19 , ARG H:20 , ILE H:21 , ASP H:43 , THR H:44 , ALA H:79 , THR H:80 , SER H:82 , HIS H:85 , GLN H:88 , GLU H:102 , LYS H:103 , GLN H:131 , TRP H:174 , ARG H:175 , HIS H:191 , HP7 H:550
BINDING SITE FOR RESIDUE NAI H 500
16
BC7
SOFTWARE
ARG H:20 , LYS H:103 , GLN H:131 , TRP H:162 , THR H:163 , ARG H:164 , PRO H:165 , TYR H:168 , ASN H:187 , GLN H:188 , HIS H:191 , GLN H:246 , ASN H:247 , NAI H:500 , HOH H:538 , HOH H:539
BINDING SITE FOR RESIDUE HP7 H 550
17
CC8
SOFTWARE
ASP D:284 , ARG D:287 , ARG M:20 , LYS M:103 , GLN M:131 , TRP M:162 , THR M:163 , ARG M:164 , PRO M:165 , TYR M:168 , ASN M:187 , GLN M:188 , HIS M:191 , GLN M:246 , ASN M:247 , HOH M:469 , NAI M:500
BINDING SITE FOR RESIDUE HP7 M 550
18
DC1
SOFTWARE
ARG A:287 , ARG N:20 , LYS N:103 , ASN N:132 , TRP N:162 , THR N:163 , ARG N:164 , PRO N:165 , TYR N:168 , ASN N:187 , GLN N:188 , HIS N:191 , GLN N:246 , ASN N:247 , HOH N:454 , HOH N:494 , HOH N:499 , NAI N:500 , HOH N:501
BINDING SITE FOR RESIDUE HP7 N 550
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
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All Exon Boundaries
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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
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(2, 32)
Info
all PFAM domains
1a: PFAM_GFO_IDH_MocA_3q2kP01 (P:11-130)
1b: PFAM_GFO_IDH_MocA_3q2kP02 (P:11-130)
1c: PFAM_GFO_IDH_MocA_3q2kP03 (P:11-130)
1d: PFAM_GFO_IDH_MocA_3q2kP04 (P:11-130)
1e: PFAM_GFO_IDH_MocA_3q2kP05 (P:11-130)
1f: PFAM_GFO_IDH_MocA_3q2kP06 (P:11-130)
1g: PFAM_GFO_IDH_MocA_3q2kP07 (P:11-130)
1h: PFAM_GFO_IDH_MocA_3q2kP08 (P:11-130)
1i: PFAM_GFO_IDH_MocA_3q2kP09 (P:11-130)
1j: PFAM_GFO_IDH_MocA_3q2kP10 (P:11-130)
1k: PFAM_GFO_IDH_MocA_3q2kP11 (P:11-130)
1l: PFAM_GFO_IDH_MocA_3q2kP12 (P:11-130)
1m: PFAM_GFO_IDH_MocA_3q2kP13 (P:11-130)
1n: PFAM_GFO_IDH_MocA_3q2kP14 (P:11-130)
1o: PFAM_GFO_IDH_MocA_3q2kP15 (P:11-130)
1p: PFAM_GFO_IDH_MocA_3q2kP16 (P:11-130)
2a: PFAM_GFO_IDH_MocA_C_3q2kP17 (P:142-257)
2b: PFAM_GFO_IDH_MocA_C_3q2kP18 (P:142-257)
2c: PFAM_GFO_IDH_MocA_C_3q2kP19 (P:142-257)
2d: PFAM_GFO_IDH_MocA_C_3q2kP20 (P:142-257)
2e: PFAM_GFO_IDH_MocA_C_3q2kP21 (P:142-257)
2f: PFAM_GFO_IDH_MocA_C_3q2kP22 (P:142-257)
2g: PFAM_GFO_IDH_MocA_C_3q2kP23 (P:142-257)
2h: PFAM_GFO_IDH_MocA_C_3q2kP24 (P:142-257)
2i: PFAM_GFO_IDH_MocA_C_3q2kP25 (P:142-257)
2j: PFAM_GFO_IDH_MocA_C_3q2kP26 (P:142-257)
2k: PFAM_GFO_IDH_MocA_C_3q2kP27 (P:142-257)
2l: PFAM_GFO_IDH_MocA_C_3q2kP28 (P:142-257)
2m: PFAM_GFO_IDH_MocA_C_3q2kP29 (P:142-257)
2n: PFAM_GFO_IDH_MocA_C_3q2kP30 (P:142-257)
2o: PFAM_GFO_IDH_MocA_C_3q2kP31 (P:142-257)
2p: PFAM_GFO_IDH_MocA_C_3q2kP32 (P:142-257)
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Clan
:
NADP_Rossmann
(1239)
Family
:
GFO_IDH_MocA
(25)
Bordetella pertussis
(1)
1a
GFO_IDH_MocA-3q2kP01
P:11-130
1b
GFO_IDH_MocA-3q2kP02
P:11-130
1c
GFO_IDH_MocA-3q2kP03
P:11-130
1d
GFO_IDH_MocA-3q2kP04
P:11-130
1e
GFO_IDH_MocA-3q2kP05
P:11-130
1f
GFO_IDH_MocA-3q2kP06
P:11-130
1g
GFO_IDH_MocA-3q2kP07
P:11-130
1h
GFO_IDH_MocA-3q2kP08
P:11-130
1i
GFO_IDH_MocA-3q2kP09
P:11-130
1j
GFO_IDH_MocA-3q2kP10
P:11-130
1k
GFO_IDH_MocA-3q2kP11
P:11-130
1l
GFO_IDH_MocA-3q2kP12
P:11-130
1m
GFO_IDH_MocA-3q2kP13
P:11-130
1n
GFO_IDH_MocA-3q2kP14
P:11-130
1o
GFO_IDH_MocA-3q2kP15
P:11-130
1p
GFO_IDH_MocA-3q2kP16
P:11-130
Clan
:
ox_reductase_C
(19)
Family
:
GFO_IDH_MocA_C
(19)
Bordetella pertussis
(1)
2a
GFO_IDH_MocA_C-3q2kP17
P:142-257
2b
GFO_IDH_MocA_C-3q2kP18
P:142-257
2c
GFO_IDH_MocA_C-3q2kP19
P:142-257
2d
GFO_IDH_MocA_C-3q2kP20
P:142-257
2e
GFO_IDH_MocA_C-3q2kP21
P:142-257
2f
GFO_IDH_MocA_C-3q2kP22
P:142-257
2g
GFO_IDH_MocA_C-3q2kP23
P:142-257
2h
GFO_IDH_MocA_C-3q2kP24
P:142-257
2i
GFO_IDH_MocA_C-3q2kP25
P:142-257
2j
GFO_IDH_MocA_C-3q2kP26
P:142-257
2k
GFO_IDH_MocA_C-3q2kP27
P:142-257
2l
GFO_IDH_MocA_C-3q2kP28
P:142-257
2m
GFO_IDH_MocA_C-3q2kP29
P:142-257
2n
GFO_IDH_MocA_C-3q2kP30
P:142-257
2o
GFO_IDH_MocA_C-3q2kP31
P:142-257
2p
GFO_IDH_MocA_C-3q2kP32
P:142-257
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