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1GMO
Biol. Unit 1
Info
Asym.Unit (249 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (63 KB)
Biol.Unit 3 (62 KB)
Biol.Unit 4 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR
Authors
:
D. Lietha, D. Y. Chirgadze, B. Mulloy, T. L. Blundell, E. Gherardi
Date
:
20 Sep 01 (Deposition) - 02 Oct 01 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Hormone, Growth Factor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Lietha, D. Y. Chirgadze, B. Mulloy, T. L. Blundell, E. Gherardi
Crystal Structures Of Nk1-Heparin Complexes Reveal The Basi For Nk1 Activity And Enable Engineering Of Potent Agonists Of The Met Receptor
Embo J. V. 20 5543 2001
[
close entry info
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Hetero Components
(4, 25)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
1c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
1d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
1e: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEe)
1f: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEf)
1g: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEg)
1h: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEh)
2a: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSa)
2b: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSb)
2c: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSc)
2d: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSd)
2e: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSe)
2f: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSf)
2g: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSg)
2h: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSh)
2i: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSi)
2j: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSj)
2k: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSk)
2l: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSl)
2m: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSm)
2n: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSn)
2o: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSo)
2p: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSp)
2q: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSq)
2r: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSr)
2s: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSs)
2t: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSt)
2u: 2-O-SULFO-ALPHA-L-IDOPYRANURONIC A... (IDSu)
3a: N,O6-DISULFO-GLUCOSAMINE (SGNa)
3b: N,O6-DISULFO-GLUCOSAMINE (SGNb)
3c: N,O6-DISULFO-GLUCOSAMINE (SGNc)
3d: N,O6-DISULFO-GLUCOSAMINE (SGNd)
3e: N,O6-DISULFO-GLUCOSAMINE (SGNe)
3f: N,O6-DISULFO-GLUCOSAMINE (SGNf)
3g: N,O6-DISULFO-GLUCOSAMINE (SGNg)
3h: N,O6-DISULFO-GLUCOSAMINE (SGNh)
3i: N,O6-DISULFO-GLUCOSAMINE (SGNi)
3j: N,O6-DISULFO-GLUCOSAMINE (SGNj)
3k: N,O6-DISULFO-GLUCOSAMINE (SGNk)
3l: N,O6-DISULFO-GLUCOSAMINE (SGNl)
3m: N,O6-DISULFO-GLUCOSAMINE (SGNm)
3n: N,O6-DISULFO-GLUCOSAMINE (SGNn)
3o: N,O6-DISULFO-GLUCOSAMINE (SGNo)
3p: N,O6-DISULFO-GLUCOSAMINE (SGNp)
3q: N,O6-DISULFO-GLUCOSAMINE (SGNq)
3r: N,O6-DISULFO-GLUCOSAMINE (SGNr)
3s: N,O6-DISULFO-GLUCOSAMINE (SGNs)
3t: N,O6-DISULFO-GLUCOSAMINE (SGNt)
3u: N,O6-DISULFO-GLUCOSAMINE (SGNu)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
2
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
IDS
11
Ligand/Ion
2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3
SGN
10
Ligand/Ion
N,O6-DISULFO-GLUCOSAMINE
4
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AD8 (SOFTWARE)
07: AD9 (SOFTWARE)
08: AE1 (SOFTWARE)
09: AE2 (SOFTWARE)
10: AE3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:164 , GLY A:169 , ASP A:171 , LEU A:172 , GLN A:173
binding site for residue SO4 A 307
02
AC2
SOFTWARE
PHE A:162 , GLU A:183 , GLU A:184 , GLY A:185 , GLY A:186 , TRP A:188 , PHE A:190 , ARG A:197 , TYR A:198 , VAL A:200 , GLU C:111 , PHE C:112
binding site for residue EPE A 308
03
AC3
SOFTWARE
ARG B:126 , ILE B:129 , ILE B:130 , GLY B:133 , ARG B:134 , SER B:135 , TYR B:136 , HOH B:412
binding site for residue SO4 B 308
04
AC4
SOFTWARE
PHE B:162 , GLU B:183 , GLU B:184 , GLY B:185 , GLY B:186 , TRP B:188 , PHE B:190 , ARG B:197 , TYR B:198 , HOH B:407
binding site for residue EPE B 317
05
AC5
SOFTWARE
SGN B:310 , ARG C:126 , ILE C:129 , ILE C:130 , GLY C:133 , ARG C:134 , SER C:135 , TYR C:136
binding site for residue SO4 C 301
06
AD8
SOFTWARE
LYS A:60 , THR A:61 , LYS A:62 , GLN A:95 , HOH A:408 , ILE E:59 , LYS E:60 , THR E:61 , LYS E:62 , LYS E:63 , VAL E:64 , ARG E:73 , GLY E:79
binding site for Poly-Saccharide residues IDS A 301 through SGN A 306
07
AD9
SOFTWARE
LYS A:60 , THR A:61 , LYS A:62 , GLN A:95 , PRO A:164 , GLY A:169 , ASP A:171 , LEU A:172 , GLN A:173 , HOH A:408 , TYR B:167 , ARG B:168 , GLY B:169 , LYS B:170 , PRO B:180 , ARG B:181 , GLY B:182 , ILE E:59 , LYS E:60 , THR E:61 , LYS E:62 , LYS E:63 , VAL E:64 , ARG E:73 , GLY E:79 , LYS H:60 , THR H:61 , LYS H:62 , LYS H:63 , GLN H:69 , LYS H:78 , GLY H:79
binding site for Poly-Saccharide residues IDS B 301 through IDS B 307
08
AE1
SOFTWARE
TYR A:167 , ARG A:168 , LYS A:170 , ILE B:59 , LYS B:60 , THR B:61 , LYS B:62 , LYS B:63 , VAL B:64 , ARG B:73 , ARG B:76 , LYS B:78 , GLY B:79 , TYR B:167 , LYS B:170 , PRO B:180 , ARG B:181 , GLY B:182 , IDS B:301 , HOH B:414 , HOH B:421 , LYS C:132 , ARG C:134 , GLU C:184 , SO4 C:301 , LYS H:60 , THR H:61 , LYS H:62 , LYS H:63 , GLN H:69 , LYS H:78 , GLY H:79
binding site for Poly-Saccharide residues IDS B 309 through SGN B 316
09
AE2
SOFTWARE
TYR A:167 , ARG A:168 , LYS A:170 , ILE B:59 , LYS B:60 , THR B:61 , LYS B:62 , LYS B:63 , VAL B:64 , ARG B:73 , ARG B:76 , LYS B:78 , GLY B:79 , ARG B:126 , ILE B:129 , ILE B:130 , GLY B:133 , ARG B:134 , SER B:135 , TYR B:136 , TYR B:167 , LYS B:170 , PRO B:180 , ARG B:181 , GLY B:182 , IDS B:301 , HOH B:412 , HOH B:414 , HOH B:421 , LYS C:60 , THR C:61 , LYS C:62 , LYS C:63 , GLN C:69 , ARG C:73 , ARG C:76 , LYS C:78 , GLY C:79 , LYS C:132 , ARG C:134 , GLU C:183 , GLU C:184 , GLY C:185 , GLY C:186 , TRP C:188 , PHE C:190 , ARG C:197 , TYR C:198 , SO4 C:301 , HOH C:407 , HOH C:410 , HOH C:415 , HOH C:418 , HOH C:419 , SER D:166 , TYR D:167 , ARG D:168 , GLU E:159 , ARG E:197 , ARG F:134 , TYR F:167 , ARG F:168 , ARG F:181 , GLY F:182 , SER G:154 , ILE G:156 , LYS H:60 , THR H:61 , LYS H:62 , LYS H:63 , GLN H:69 , LYS H:78 , GLY H:79
binding site for Poly-Saccharide residues SGN C 302 through SGN C 310
10
AE3
SOFTWARE
SGN B:310 , LYS C:60 , THR C:61 , LYS C:62 , LYS C:63 , GLN C:69 , ARG C:73 , ARG C:76 , LYS C:78 , GLY C:79 , ARG C:126 , ILE C:129 , ILE C:130 , GLY C:133 , ARG C:134 , SER C:135 , TYR C:136 , HOH C:415 , HOH C:418 , HOH C:419 , SER D:166 , TYR D:167 , ARG D:168 , ILE F:59 , THR F:61 , LYS F:62 , LYS F:63 , VAL F:64 , GLN F:69 , ARG F:73 , LYS F:78 , GLY F:79 , ARG F:126 , ILE F:129 , ILE F:130 , GLY F:133 , ARG F:134 , SER F:135 , TYR F:136 , TYR F:167 , ARG F:168 , GLY F:169 , ASP F:171 , LEU F:172 , GLN F:173 , ARG F:181 , GLY F:182 , GLU F:183 , TRP F:188 , TYR F:198 , GLU F:199 , VAL F:200 , HOH F:405 , SER G:154 , ILE G:156 , GLU G:159 , ARG H:181
binding site for Poly-Saccharide residues SGN F 301 through IDS F 306
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_014570 (S153I, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_014570
S
153
I
HGF_HUMAN
Polymorphism
17566
A/B
S
153
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: PAN (A:37-123,B:37-123)
2: KRINGLE_2 (A:127-206,B:127-206)
3: KRINGLE_1 (A:176-189,B:176-189)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PAN
PS50948
PAN/Apple domain profile.
HGF_HUMAN
37-123
2
A:37-123
B:37-123
-
-
-
-
2
KRINGLE_2
PS50070
Kringle domain profile.
HGF_HUMAN
127-206
210-288
304-383
390-469
2
A:127-206
B:127-206
-
-
-
-
-
-
-
-
-
3
KRINGLE_1
PS00021
Kringle domain signature.
HGF_HUMAN
176-189
259-271
353-365
439-452
2
A:176-189
B:176-189
-
-
-
-
-
-
-
-
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1gmoa1 (A:37-125)
1b: SCOP_d1gmob1 (B:37-125)
1c: SCOP_d1gmoc1 (C:37-125)
1d: SCOP_d1gmod1 (D:37-125)
1e: SCOP_d1gmoe1 (E:37-125)
1f: SCOP_d1gmof1 (F:37-125)
1g: SCOP_d1gmog1 (G:38-125)
1h: SCOP_d1gmoh1 (H:38-125)
2a: SCOP_d1gmoa2 (A:126-208)
2b: SCOP_d1gmob2 (B:126-208)
2c: SCOP_d1gmoc2 (C:126-208)
2d: SCOP_d1gmod2 (D:126-208)
2e: SCOP_d1gmoe2 (E:126-209)
2f: SCOP_d1gmof2 (F:126-209)
2g: SCOP_d1gmog2 (G:126-208)
2h: SCOP_d1gmoh2 (H:126-208)
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)
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Folds
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)
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)
Superfamilies
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)
(
)
Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Hairpin loop containing domain-like
(17)
Superfamily
:
Hairpin loop containing domain-like
(17)
Family
:
Hairpin loop containing domain
(15)
Protein domain
:
Hepatocyte growth factor
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d1gmoa1
A:37-125
1b
d1gmob1
B:37-125
1c
d1gmoc1
C:37-125
1d
d1gmod1
D:37-125
1e
d1gmoe1
E:37-125
1f
d1gmof1
F:37-125
1g
d1gmog1
G:38-125
1h
d1gmoh1
H:38-125
Fold
:
Kringle-like
(68)
Superfamily
:
Kringle-like
(68)
Family
:
Kringle modules
(54)
Protein domain
:
NK1 fragment of hepatocyte growth factor
(8)
Human (Homo sapiens) [TaxId: 9606]
(8)
2a
d1gmoa2
A:126-208
2b
d1gmob2
B:126-208
2c
d1gmoc2
C:126-208
2d
d1gmod2
D:126-208
2e
d1gmoe2
E:126-209
2f
d1gmof2
F:126-209
2g
d1gmog2
G:126-208
2h
d1gmoh2
H:126-208
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1gmoH01 (H:38-125)
1b: CATH_1gmoB01 (B:37-125)
1c: CATH_1gmoC01 (C:37-125)
1d: CATH_1gmoD01 (D:37-125)
1e: CATH_1gmoE01 (E:37-125)
1f: CATH_1gmoF01 (F:37-125)
1g: CATH_1gmoG01 (G:38-125)
1h: CATH_1gmoA01 (A:37-125)
2a: CATH_1gmoE02 (E:126-209)
2b: CATH_1gmoF02 (F:126-209)
2c: CATH_1gmoA02 (A:126-208)
2d: CATH_1gmoB02 (B:126-208)
2e: CATH_1gmoC02 (C:126-208)
2f: CATH_1gmoD02 (D:126-208)
2g: CATH_1gmoH02 (H:126-208)
2h: CATH_1gmoG02 (G:126-207)
View:
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Architectures
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Topologies
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
Hepatocyte Growth Factor
(13)
Homologous Superfamily
:
Hepatocyte Growth Factor
(13)
Human (Homo sapiens)
(9)
1a
1gmoH01
H:38-125
1b
1gmoB01
B:37-125
1c
1gmoC01
C:37-125
1d
1gmoD01
D:37-125
1e
1gmoE01
E:37-125
1f
1gmoF01
F:37-125
1g
1gmoG01
G:38-125
1h
1gmoA01
A:37-125
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Plasminogen Kringle 4
(42)
Homologous Superfamily
:
Plasminogen Kringle 4
(42)
Human (Homo sapiens)
(37)
2a
1gmoE02
E:126-209
2b
1gmoF02
F:126-209
2c
1gmoA02
A:126-208
2d
1gmoB02
B:126-208
2e
1gmoC02
C:126-208
2f
1gmoD02
D:126-208
2g
1gmoH02
H:126-208
2h
1gmoG02
G:126-207
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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