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2WUB
Biol. Unit 1
Info
Asym.Unit (216 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (108 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HGFA IN COMPLEX WITH THE ALLOSTERIC NON-INHIBITORY ANTIBODY FAB40.DELTATRP
Authors
:
R. Ganesan, C. Eigenbrot, S. Shia
Date
:
01 Oct 09 (Deposition) - 15 Dec 09 (Release) - 28 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,H,L,Q,R
Biol. Unit 1: C,D,Q,R (1x)
Biol. Unit 2: A,B,H,L (1x)
Keywords
:
Hydrolase Immune System Complex, Disulfide Bond, Serine Protease, Egf-Like Domain, Allosteric Inhibitor, Kringle, Zymogen, Protease, Secreted, Antibody, Hydrolase, Fab Complex, Polymorphism, Glycoprotein
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Reference
:
R. Ganesan, C. Eigenbrot, Y. Wu, W. C. Liang, S. Shia, M. T. Lipari, D. Kirchhofer
Unraveling The Allosteric Mechanism Of Serine Protease Inhibition By An Antibody
Structure V. 17 1614 2009
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
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No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(1, 1)
Info
All Sites
1: AC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ASN C:74 , HOH C:2023
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 74 RESIDUES 1245 TO 1247
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_024295 (R241Q, chain C, )
2: VAR_024294 (R111CH, chain C, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024295
R
644
Q
HGFA_HUMAN
Polymorphism
2498323
C
R
241
Q
2
UniProt
VAR_024294
R
509
H
HGFA_HUMAN
Polymorphism
16844401
C
R
111C
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (C:16-243)
2: TRYPSIN_HIS (C:53-58)
3: TRYPSIN_SER (C:189-200)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
HGFA_HUMAN
408-646
1
-
C:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
HGFA_HUMAN
443-448
1
-
C:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
HGFA_HUMAN
592-603
1
-
C:189-200
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Exons
(0, 0)
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2wubl1 (L:1-107)
1b: SCOP_d2wubq1 (Q:1-107)
2a: SCOP_d2wubl2 (L:108-214)
2b: SCOP_d2wubq2 (Q:108-214)
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Protein Domains
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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
d2wubl1
L:1-107
1b
d2wubq1
Q:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d2wubl2
L:108-214
2b
d2wubq2
Q:108-214
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CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_2wubC01 (C:16-27,C:121-230)
1b: CATH_2wubA01 (A:16-27,A:121-230)
1c: CATH_2wubA02 (A:28-120,A:231-244)
1d: CATH_2wubC02 (C:28-120,C:231-244)
2a: CATH_2wubL02 (L:109-214)
2b: CATH_2wubH02 (H:114-217)
2c: CATH_2wubR02 (R:114-209)
2d: CATH_2wubH01 (H:1-113)
2e: CATH_2wubR01 (R:1-113)
2f: CATH_2wubQ02 (Q:109-214)
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Organisms
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Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
1a
2wubC01
C:16-27,C:121-230
1b
2wubA01
A:16-27,A:121-230
1c
2wubA02
A:28-120,A:231-244
1d
2wubC02
C:28-120,C:231-244
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2wubL02
L:109-214
2b
2wubH02
H:114-217
2c
2wubR02
R:114-209
2d
2wubH01
H:1-113
2e
2wubR01
R:1-113
2f
2wubQ02
Q:109-214
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Trypsin_2wubC01 (C:16-238)
1b: PFAM_Trypsin_2wubC02 (C:16-238)
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Clan
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Peptidase_PA
(797)
Family
:
Trypsin
(679)
Homo sapiens (Human)
(339)
1a
Trypsin-2wubC01
C:16-238
1b
Trypsin-2wubC02
C:16-238
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (216 KB)
Header - Asym.Unit
Biol.Unit 1 (107 KB)
Header - Biol.Unit 1
Biol.Unit 2 (108 KB)
Header - Biol.Unit 2
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