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3GBM
Biol. Unit 1
Info
Asym.Unit (302 KB)
Biol.Unit 1 (433 KB)
Biol.Unit 2 (414 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FAB CR6261 IN COMPLEX WITH A H5N1 INFLUENZA VIRUS HEMAGGLUTININ.
Authors
:
D. C. Ekiert, M. A. Elsliger, I. A. Wilson
Date
:
20 Feb 09 (Deposition) - 10 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,H,I,L,M
Biol. Unit 1: A,B,H,L (3x)
Biol. Unit 2: C,D,I,M (3x)
Keywords
:
Hemagglutinin, Fab, Neutralizing Antibodies, Antibody, Avian Flu, Envelope Protein, Fusion Protein, Viral Protein - Immune System Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
D. C. Ekiert, G. Bhabha, M. A. Elsliger, R. H. Friesen, M. Jongeneelen, M. Throsby, J. Goudsmit, I. A. Wilson
Antibody Recognition Of A Highly Conserved Influenza Virus Epitope.
Science V. 324 246 2009
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Hetero Components
(4, 24)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: GLYCEROL (GOLa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
3
Ligand/Ion
GLYCEROL
4
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC6 (SOFTWARE)
6: AC7 (SOFTWARE)
7: AC8 (SOFTWARE)
8: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:33 , HOH A:344 , HOH A:360
BINDING SITE FOR RESIDUE NAG A 1
2
AC2
SOFTWARE
NAG A:2 , ASN A:169 , SER A:221 , ASN A:240 , ASP A:241 , ALA A:242
BINDING SITE FOR RESIDUE NAG A 334
3
AC3
SOFTWARE
NAG A:334
BINDING SITE FOR RESIDUE NAG A 2
4
AC5
SOFTWARE
ASN A:158 , GLY L:200 , THR L:204
BINDING SITE FOR RESIDUE NAG A 335
5
AC6
SOFTWARE
ASP A:27 , ARG A:313 , VAL A:315 , ASN B:104
BINDING SITE FOR RESIDUE EDO A 336
6
AC7
SOFTWARE
GLU B:147 , ASN B:154
BINDING SITE FOR RESIDUE NAG B 182
7
AC8
SOFTWARE
ALA B:36 , ASP B:37 , LYS B:38 , GLU B:39 , ARG B:153 , ASN B:154
BINDING SITE FOR RESIDUE GOL B 183
8
AC9
SOFTWARE
HIS A:18 , ASN A:20 , ASN A:21 , HIS A:38 , PHE H:54
BINDING SITE FOR RESIDUE BMA C 4
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
Info
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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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d3gbml1 (L:3-105)
1b: SCOP_d3gbmm1 (M:3-106A)
2a: SCOP_d3gbml2 (L:108-213)
2b: SCOP_d3gbmm2 (M:112-211)
3a: SCOP_d3gbma_ (A:)
3b: SCOP_d3gbmc_ (C:)
4a: SCOP_d3gbmb_ (B:)
4b: SCOP_d3gbmd_ (D:)
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Classes
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)
(
)
Folds
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d3gbml1
L:3-105
1b
d3gbmm1
M:3-106A
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d3gbml2
L:108-213
2b
d3gbmm2
M:112-211
Fold
:
Viral protein domain
(195)
Superfamily
:
Viral protein domain
(195)
Family
:
Influenza hemagglutinin headpiece
(152)
Protein domain
:
Hemagglutinin
(109)
Influenza a virus (a/viet nam/1203/2004(h5n1)) [TaxId: 284218]
(2)
3a
d3gbma_
A:
3b
d3gbmc_
C:
Class
:
Coiled coil proteins
(689)
Fold
:
Stalk segment of viral fusion proteins
(231)
Superfamily
:
Influenza hemagglutinin (stalk)
(172)
Family
:
Influenza hemagglutinin (stalk)
(161)
Protein domain
:
Influenza hemagglutinin (stalk)
(102)
Influenza A virus, different strains [TaxId: 11320]
(93)
4a
d3gbmb_
B:
4b
d3gbmd_
D:
[
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CATH Domains
(4, 12)
Info
all CATH domains
1a: CATH_3gbmA02 (A:57-272)
1b: CATH_3gbmC02 (C:57-272)
2a: CATH_3gbmB00 (B:1-177)
2b: CATH_3gbmD00 (D:1-173)
3a: CATH_3gbmC01 (C:9-56,C:273-324)
3b: CATH_3gbmA01 (A:8-56,A:273-324)
4a: CATH_3gbmH02 (H:114-227)
4b: CATH_3gbmI02 (I:114-223)
4c: CATH_3gbmH01 (H:1-113)
4d: CATH_3gbmI01 (I:1-113)
4e: CATH_3gbmL02 (L:108-213)
4f: CATH_3gbmM02 (M:106-211)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Hemagglutinin (Ha1 Chain); Chain: A; domain 1
(59)
Homologous Superfamily
:
[code=3.90.209.20, no name defined]
(59)
A/viet nam/1203/2004(h5n1) (Influenza a virus (a/viet nam/1203/2004(h5n1)))
(1)
1a
3gbmA02
A:57-272
1b
3gbmC02
C:57-272
Topology
:
Hemagglutinin Ectodomain; Chain B
(70)
Homologous Superfamily
:
[code=3.90.20.10, no name defined]
(69)
A/viet nam/1203/2004(h5n1) (Influenza a virus (a/viet nam/1203/2004(h5n1)))
(1)
2a
3gbmB00
B:1-177
2b
3gbmD00
D:1-173
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Hemagglutinin; Chain A, domain 2
(27)
Homologous Superfamily
:
Hemagglutinin Chain A, Domain 2
(27)
A/viet nam/1203/2004(h5n1) (Influenza a virus (a/viet nam/1203/2004(h5n1)))
(1)
3a
3gbmC01
C:9-56,C:273-324
3b
3gbmA01
A:8-56,A:273-324
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
A/viet nam/1203/2004(h5n1) (Influenza a virus (a/viet nam/1203/2004(h5n1)))
(1)
4a
3gbmH02
H:114-227
4b
3gbmI02
I:114-223
4c
3gbmH01
H:1-113
4d
3gbmI01
I:1-113
4e
3gbmL02
L:108-213
4f
3gbmM02
M:106-211
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (302 KB)
Header - Asym.Unit
Biol.Unit 1 (433 KB)
Header - Biol.Unit 1
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