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3GBM
Asym. Unit
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, 14)
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
2
Ligand/Ion
BETA-D-MANNOSE
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
1
Ligand/Ion
GLYCEROL
4
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:33 , HOH A:344 , HOH A:360
BINDING SITE FOR RESIDUE NAG A 1
02
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
03
AC3
SOFTWARE
NAG A:334
BINDING SITE FOR RESIDUE NAG A 2
04
AC4
SOFTWARE
HIS C:18 , ASN C:20 , ASN C:21 , HIS C:38 , PHE I:54
BINDING SITE FOR RESIDUE BMA A 4
05
AC5
SOFTWARE
ASN A:158 , GLY L:200 , THR L:204
BINDING SITE FOR RESIDUE NAG A 335
06
AC6
SOFTWARE
ASP A:27 , ARG A:313 , VAL A:315 , ASN B:104
BINDING SITE FOR RESIDUE EDO A 336
07
AC7
SOFTWARE
GLU B:147 , ASN B:154
BINDING SITE FOR RESIDUE NAG B 182
08
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
09
AC9
SOFTWARE
HIS A:18 , ASN A:20 , ASN A:21 , HIS A:38 , PHE H:54
BINDING SITE FOR RESIDUE BMA C 4
10
BC1
SOFTWARE
NAG C:2 , ASN C:169 , SER C:221 , ASN C:240 , ASP C:241 , ALA C:242
BINDING SITE FOR RESIDUE NAG C 1
11
BC2
SOFTWARE
NAG C:1
BINDING SITE FOR RESIDUE NAG C 2
12
BC3
SOFTWARE
GLN C:25 , ASN C:33
BINDING SITE FOR RESIDUE NAG C 334
13
BC4
SOFTWARE
VAL C:26 , ASP C:27 , ARG C:313 , LEU C:314 , VAL C:315 , VAL D:100 , ASN D:104
BINDING SITE FOR RESIDUE EDO C 335
14
BC5
SOFTWARE
GLU D:147 , GLU D:150 , ASN D:154 , THR D:156
BINDING SITE FOR RESIDUE NAG D 182
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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Exons
(0, 0)
Info
All Exons
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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.
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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(
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Superfamilies
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)
(
)
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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Protein & NOT PROSITE
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Chain C
Chain D
Chain H
Chain I
Chain L
Chain M
Asymmetric Unit 1
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