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2FRV
Asym. Unit
Info
Asym.Unit (759 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (135 KB)
Biol.Unit 3 (135 KB)
Biol.Unit 4 (136 KB)
Biol.Unit 5 (136 KB)
Biol.Unit 6 (136 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
Authors
:
A. Volbeda, M. Frey, J. C. Fontecilla-Camps
Date
:
10 Jun 97 (Deposition) - 17 Jun 98 (Release) - 24 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.54
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,L,S
Biol. Unit 1: L,S (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Biol. Unit 4: E,F (1x)
Biol. Unit 5: G,H (1x)
Biol. Unit 6: I,J (1x)
Keywords
:
Oxidoreductase, Ni-Fe Hydrogenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, E. Garcin, C. Piras, A. L. De Lacey, V. M. Fernandez, E. C. Hatchikian, M. Frey, J. C. Fontecilla-Camps
Structure Of The [Nife] Hydrogenase Active Site: Evidence For Biologically Uncommon Fe Ligands
J. Am. Chem. Soc. V. 118 12989 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 42)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
1c: FE3-S4 CLUSTER (F3Sc)
1d: FE3-S4 CLUSTER (F3Sd)
1e: FE3-S4 CLUSTER (F3Se)
1f: FE3-S4 CLUSTER (F3Sf)
2a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
2b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
2c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
2d: CARBONMONOXIDE-(DICYANO) IRON (FCOd)
2e: CARBONMONOXIDE-(DICYANO) IRON (FCOe)
2f: CARBONMONOXIDE-(DICYANO) IRON (FCOf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
4c: NICKEL (II) ION (NIc)
4d: NICKEL (II) ION (NId)
4e: NICKEL (II) ION (NIe)
4f: NICKEL (II) ION (NIf)
5a: OXYGEN ATOM (Oa)
5b: OXYGEN ATOM (Ob)
5c: OXYGEN ATOM (Oc)
5d: OXYGEN ATOM (Od)
5e: OXYGEN ATOM (Oe)
5f: OXYGEN ATOM (Of)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
6d: IRON/SULFUR CLUSTER (SF4d)
6e: IRON/SULFUR CLUSTER (SF4e)
6f: IRON/SULFUR CLUSTER (SF4f)
6g: IRON/SULFUR CLUSTER (SF4g)
6h: IRON/SULFUR CLUSTER (SF4h)
6i: IRON/SULFUR CLUSTER (SF4i)
6j: IRON/SULFUR CLUSTER (SF4j)
6k: IRON/SULFUR CLUSTER (SF4k)
6l: IRON/SULFUR CLUSTER (SF4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
6
Ligand/Ion
FE3-S4 CLUSTER
2
FCO
6
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
3
MG
6
Ligand/Ion
MAGNESIUM ION
4
NI
6
Ligand/Ion
NICKEL (II) ION
5
O
6
Ligand/Ion
OXYGEN ATOM
6
SF4
12
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(43, 43)
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: ACT (UNKNOWN)
11: BC1 (SOFTWARE)
12: BC2 (SOFTWARE)
13: BC3 (SOFTWARE)
14: BC4 (SOFTWARE)
15: BC5 (SOFTWARE)
16: BC6 (SOFTWARE)
17: BC7 (SOFTWARE)
18: BC8 (SOFTWARE)
19: BC9 (SOFTWARE)
20: CC1 (SOFTWARE)
21: CC2 (SOFTWARE)
22: CC3 (SOFTWARE)
23: CC4 (SOFTWARE)
24: CC5 (SOFTWARE)
25: CC6 (SOFTWARE)
26: CC7 (SOFTWARE)
27: CC8 (SOFTWARE)
28: CC9 (SOFTWARE)
29: DC1 (SOFTWARE)
30: DC2 (SOFTWARE)
31: DC3 (SOFTWARE)
32: DC4 (SOFTWARE)
33: DC5 (SOFTWARE)
34: DC6 (SOFTWARE)
35: DC7 (SOFTWARE)
36: DC8 (SOFTWARE)
37: DC9 (SOFTWARE)
38: EC1 (SOFTWARE)
39: EC2 (SOFTWARE)
40: EC3 (SOFTWARE)
41: EC4 (SOFTWARE)
42: EC5 (SOFTWARE)
43: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS L:65 , CYS L:68 , CYS L:530 , CYS L:533 , FCO L:537 , O L:539
BINDING SITE FOR RESIDUE NI L 538
02
AC2
SOFTWARE
CYS B:65 , CYS B:68 , CYS B:530 , CYS B:533 , FCO B:537 , O B:539
BINDING SITE FOR RESIDUE NI B 538
03
AC3
SOFTWARE
CYS D:65 , CYS D:68 , CYS D:530 , CYS D:533 , FCO D:537 , O D:539
BINDING SITE FOR RESIDUE NI D 538
04
AC4
SOFTWARE
CYS F:65 , CYS F:68 , CYS F:530 , CYS F:533 , FCO F:537 , O F:539
BINDING SITE FOR RESIDUE NI F 538
05
AC5
SOFTWARE
CYS H:65 , CYS H:68 , CYS H:530 , CYS H:533 , FCO H:537 , O H:539
BINDING SITE FOR RESIDUE NI H 538
06
AC6
SOFTWARE
CYS J:65 , CYS J:68 , CYS J:530 , CYS J:533 , FCO J:537 , O J:539
BINDING SITE FOR RESIDUE NI J 538
07
AC7
SOFTWARE
GLU L:46 , LEU L:482 , HIS L:536 , HOH L:5011 , HOH L:5012 , HOH L:5013
BINDING SITE FOR RESIDUE MG L 540
08
AC8
SOFTWARE
GLU B:46 , LEU B:482 , HIS B:536 , HOH B:5024 , HOH B:5025 , HOH B:5026
BINDING SITE FOR RESIDUE MG B 540
09
AC9
SOFTWARE
GLU D:46 , LEU D:482 , HIS D:536 , HOH D:5037 , HOH D:5038 , HOH D:5039
BINDING SITE FOR RESIDUE MG D 540
10
ACT
UNKNOWN
CYS L:65 , CYS L:68 , CYS L:530 , CYS L:533 , FCO L:537 , NI L:538 , O L:539
NI-FE ACTIVE SITE.
11
BC1
SOFTWARE
GLU F:46 , LEU F:482 , HIS F:536 , HOH F:5050 , HOH F:5051 , HOH F:5052
BINDING SITE FOR RESIDUE MG F 540
12
BC2
SOFTWARE
GLU H:46 , LEU H:482 , HIS H:536 , HOH H:5063 , HOH H:5064 , HOH H:5065
BINDING SITE FOR RESIDUE MG H 540
13
BC3
SOFTWARE
GLU J:46 , LEU J:482 , HIS J:536 , HOH J:5076 , HOH J:5077 , HOH J:5078
BINDING SITE FOR RESIDUE MG J 540
14
BC4
SOFTWARE
HIS S:185 , CYS S:188 , CYS S:213 , LEU S:214 , CYS S:219
BINDING SITE FOR RESIDUE SF4 S 265
15
BC5
SOFTWARE
LYS L:216 , GLN L:221 , THR S:224 , ASN S:226 , CYS S:228 , PHE S:233 , TRP S:238 , PRO S:239 , CYS S:246 , ILE S:247 , CYS S:249
BINDING SITE FOR RESIDUE F3S S 266
16
BC6
SOFTWARE
ARG L:63 , HIS L:219 , GLU S:16 , CYS S:17 , CYS S:20 , GLY S:110 , THR S:111 , CYS S:112 , GLY S:147 , CYS S:148 , PRO S:149
BINDING SITE FOR RESIDUE SF4 S 267
17
BC7
SOFTWARE
CYS L:68 , VAL L:71 , HIS L:72 , ALA L:461 , PRO L:462 , ARG L:463 , LEU L:466 , VAL L:484 , PRO L:485 , SER L:486 , CYS L:533 , NI L:538 , O L:539
BINDING SITE FOR RESIDUE FCO L 537
18
BC8
SOFTWARE
CYS L:68 , ARG L:463 , CYS L:530 , CYS L:533 , FCO L:537 , NI L:538
BINDING SITE FOR RESIDUE O L 539
19
BC9
SOFTWARE
HIS A:185 , CYS A:188 , CYS A:213 , LEU A:214 , CYS A:219
BINDING SITE FOR RESIDUE SF4 A 265
20
CC1
SOFTWARE
THR A:224 , ASN A:226 , CYS A:228 , PHE A:233 , TRP A:238 , PRO A:239 , CYS A:246 , ILE A:247 , CYS A:249 , LYS B:216 , GLN B:221
BINDING SITE FOR RESIDUE F3S A 266
21
CC2
SOFTWARE
GLU A:16 , CYS A:17 , CYS A:20 , GLY A:110 , THR A:111 , CYS A:112 , GLY A:147 , CYS A:148 , PRO A:149 , ARG B:63 , HIS B:219
BINDING SITE FOR RESIDUE SF4 A 267
22
CC3
SOFTWARE
CYS B:68 , VAL B:71 , HIS B:72 , ALA B:461 , PRO B:462 , ARG B:463 , LEU B:466 , VAL B:484 , PRO B:485 , SER B:486 , CYS B:533 , NI B:538 , O B:539
BINDING SITE FOR RESIDUE FCO B 537
23
CC4
SOFTWARE
CYS B:68 , ARG B:463 , CYS B:530 , CYS B:533 , FCO B:537 , NI B:538
BINDING SITE FOR RESIDUE O B 539
24
CC5
SOFTWARE
HIS C:185 , CYS C:188 , CYS C:213 , LEU C:214 , CYS C:219
BINDING SITE FOR RESIDUE SF4 C 265
25
CC6
SOFTWARE
THR C:224 , ASN C:226 , CYS C:228 , PHE C:233 , TRP C:238 , PRO C:239 , CYS C:246 , ILE C:247 , CYS C:249 , LYS D:216 , GLN D:221
BINDING SITE FOR RESIDUE F3S C 266
26
CC7
SOFTWARE
GLU C:16 , CYS C:17 , CYS C:20 , GLY C:110 , THR C:111 , CYS C:112 , GLY C:147 , CYS C:148 , PRO C:149 , ARG D:63 , HIS D:219
BINDING SITE FOR RESIDUE SF4 C 267
27
CC8
SOFTWARE
CYS D:68 , VAL D:71 , HIS D:72 , ALA D:461 , PRO D:462 , ARG D:463 , LEU D:466 , VAL D:484 , PRO D:485 , SER D:486 , CYS D:533 , NI D:538 , O D:539
BINDING SITE FOR RESIDUE FCO D 537
28
CC9
SOFTWARE
CYS D:68 , ARG D:463 , CYS D:530 , CYS D:533 , FCO D:537 , NI D:538
BINDING SITE FOR RESIDUE O D 539
29
DC1
SOFTWARE
HIS E:185 , CYS E:188 , CYS E:213 , LEU E:214 , CYS E:219
BINDING SITE FOR RESIDUE SF4 E 265
30
DC2
SOFTWARE
THR E:224 , ASN E:226 , CYS E:228 , PHE E:233 , TRP E:238 , PRO E:239 , CYS E:246 , ILE E:247 , CYS E:249 , LYS F:216 , GLN F:221
BINDING SITE FOR RESIDUE F3S E 266
31
DC3
SOFTWARE
GLU E:16 , CYS E:17 , CYS E:20 , GLY E:110 , THR E:111 , CYS E:112 , GLY E:147 , CYS E:148 , PRO E:149 , ARG F:63 , HIS F:219
BINDING SITE FOR RESIDUE SF4 E 267
32
DC4
SOFTWARE
CYS F:68 , VAL F:71 , HIS F:72 , ALA F:461 , PRO F:462 , ARG F:463 , LEU F:466 , VAL F:484 , PRO F:485 , SER F:486 , CYS F:533 , NI F:538 , O F:539
BINDING SITE FOR RESIDUE FCO F 537
33
DC5
SOFTWARE
CYS F:68 , ARG F:463 , CYS F:530 , CYS F:533 , FCO F:537 , NI F:538
BINDING SITE FOR RESIDUE O F 539
34
DC6
SOFTWARE
HIS G:185 , CYS G:188 , CYS G:213 , LEU G:214 , CYS G:219
BINDING SITE FOR RESIDUE SF4 G 265
35
DC7
SOFTWARE
THR G:224 , ASN G:226 , CYS G:228 , PHE G:233 , TRP G:238 , PRO G:239 , CYS G:246 , ILE G:247 , CYS G:249 , LYS H:216 , GLN H:221
BINDING SITE FOR RESIDUE F3S G 266
36
DC8
SOFTWARE
GLU G:16 , CYS G:17 , CYS G:20 , GLY G:110 , THR G:111 , CYS G:112 , GLY G:147 , CYS G:148 , PRO G:149 , ARG H:63 , HIS H:219
BINDING SITE FOR RESIDUE SF4 G 267
37
DC9
SOFTWARE
CYS H:68 , VAL H:71 , HIS H:72 , ALA H:461 , PRO H:462 , ARG H:463 , LEU H:466 , VAL H:484 , PRO H:485 , SER H:486 , CYS H:533 , NI H:538 , O H:539
BINDING SITE FOR RESIDUE FCO H 537
38
EC1
SOFTWARE
CYS H:68 , ARG H:463 , CYS H:530 , CYS H:533 , FCO H:537 , NI H:538
BINDING SITE FOR RESIDUE O H 539
39
EC2
SOFTWARE
HIS I:185 , CYS I:188 , CYS I:213 , LEU I:214 , CYS I:219
BINDING SITE FOR RESIDUE SF4 I 265
40
EC3
SOFTWARE
THR I:224 , ASN I:226 , CYS I:228 , PHE I:233 , TRP I:238 , PRO I:239 , CYS I:246 , ILE I:247 , CYS I:249 , LYS J:216 , GLN J:221
BINDING SITE FOR RESIDUE F3S I 266
41
EC4
SOFTWARE
GLU I:16 , CYS I:17 , CYS I:20 , GLY I:110 , THR I:111 , CYS I:112 , GLY I:147 , CYS I:148 , PRO I:149 , ARG J:63 , HIS J:219
BINDING SITE FOR RESIDUE SF4 I 267
42
EC5
SOFTWARE
CYS J:68 , VAL J:71 , HIS J:72 , ALA J:461 , PRO J:462 , ARG J:463 , LEU J:466 , VAL J:484 , PRO J:485 , SER J:486 , CYS J:533 , NI J:538 , O J:539
BINDING SITE FOR RESIDUE FCO J 537
43
EC6
SOFTWARE
CYS J:68 , ARG J:463 , CYS J:530 , CYS J:533 , FCO J:537 , NI J:538
BINDING SITE FOR RESIDUE O J 539
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (B:43-68,D:43-68,F:43-68,H:43-68,J:...)
2: NI_HGENASE_L_2 (B:527-536,D:527-536,F:527-536,H:52...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NI_HGENASE_L_1
PS00507
Nickel-dependent hydrogenases large subunit signature 1.
PHNL_DESGI
43-68
6
B:43-68
D:43-68
F:43-68
H:43-68
J:43-68
L:43-68
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESGI
527-536
6
B:527-536
D:527-536
F:527-536
H:527-536
J:527-536
L:527-536
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2frva_ (A:)
1b: SCOP_d2frvc_ (C:)
1c: SCOP_d2frve_ (E:)
1d: SCOP_d2frvg_ (G:)
1e: SCOP_d2frvi_ (I:)
1f: SCOP_d2frvs_ (S:)
2a: SCOP_d2frvb_ (B:)
2b: SCOP_d2frvd_ (D:)
2c: SCOP_d2frvf_ (F:)
2d: SCOP_d2frvh_ (H:)
2e: SCOP_d2frvj_ (J:)
2f: SCOP_d2frvl_ (L:)
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Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
HydA/Nqo6-like
(51)
Superfamily
:
HydA/Nqo6-like
(51)
Family
:
Nickel-iron hydrogenase, small subunit
(39)
Protein domain
:
Nickel-iron hydrogenase, small subunit
(16)
Desulfovibrio gigas [TaxId: 879]
(2)
1a
d2frva_
A:
1b
d2frvc_
C:
1c
d2frve_
E:
1d
d2frvg_
G:
1e
d2frvi_
I:
1f
d2frvs_
S:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
Nickel-iron hydrogenase, large subunit
(17)
Desulfovibrio gigas [TaxId: 879]
(3)
2a
d2frvb_
B:
2b
d2frvd_
D:
2c
d2frvf_
F:
2d
d2frvh_
H:
2e
d2frvj_
J:
2f
d2frvl_
L:
[
close SCOP info
]
CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_2frvA01 (A:4-179)
1b: CATH_2frvC01 (C:4-179)
1c: CATH_2frvE01 (E:4-179)
1d: CATH_2frvG01 (G:4-179)
1e: CATH_2frvI01 (I:4-179)
1f: CATH_2frvS01 (S:4-179)
2a: CATH_2frvA02 (A:180-264)
2b: CATH_2frvC02 (C:180-264)
2c: CATH_2frvE02 (E:180-264)
2d: CATH_2frvG02 (G:180-264)
2e: CATH_2frvI02 (I:180-264)
2f: CATH_2frvS02 (S:180-264)
3a: CATH_2frvB00 (B:7-536)
3b: CATH_2frvD00 (D:7-536)
3c: CATH_2frvF00 (F:7-536)
3d: CATH_2frvH00 (H:7-536)
3e: CATH_2frvJ00 (J:7-536)
3f: CATH_2frvL00 (L:7-536)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.700, no name defined]
(28)
Desulfovibrio gigas. Organism_taxid: 879.
(2)
1a
2frvA01
A:4-179
1b
2frvC01
C:4-179
1c
2frvE01
E:4-179
1d
2frvG01
G:4-179
1e
2frvI01
I:4-179
1f
2frvS01
S:4-179
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Cytochrome-c3 Hydrogenase; Chain A, domain 2
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain A, domain 2
(28)
Desulfovibrio gigas. Organism_taxid: 879.
(2)
2a
2frvA02
A:180-264
2b
2frvC02
C:180-264
2c
2frvE02
E:180-264
2d
2frvG02
G:180-264
2e
2frvI02
I:180-264
2f
2frvS02
S:180-264
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
Desulfovibrio gigas. Organism_taxid: 879.
(2)
3a
2frvB00
B:7-536
3b
2frvD00
D:7-536
3c
2frvF00
F:7-536
3d
2frvH00
H:7-536
3e
2frvJ00
J:7-536
3f
2frvL00
L:7-536
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain L
Chain S
Asymmetric Unit 1
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(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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