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4KFE
Asym. Unit
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (447 KB)
Biol.Unit 2 (449 KB)
Biol.Unit 3 (448 KB)
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Title
:
CRYSTAL STRUCTURE OF HANSENULA POLYMORPHA COPPER AMINE OXIDASE-1 REDUCED BY METHYLAMINE AT PH 7.0
Authors
:
B. J. Johnson, E. T. Yukl, V. J. Klema, C. M. Wilmot
Date
:
26 Apr 13 (Deposition) - 21 Aug 13 (Release) - 21 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Amine Oxidase, Oxidoreductase, Peroxisome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. J. Johnson, E. T. Yukl, V. J. Klema, J. P. Klinman, C. M. Wilmot
Structural Evidence For The Semiquinone In A Copper Amine Oxidase From Hansenula Polymorpha: Implications For The Catalytic Mechanism
J. Biol. Chem. 2013
[
close entry info
]
Hetero Components
(6, 76)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
1e: COPPER (II) ION (CUe)
1f: COPPER (II) ION (CUf)
2a: FORMYL GROUP (FORa)
2b: FORMYL GROUP (FORb)
2c: FORMYL GROUP (FORc)
3a: GLYCEROL (GOLa)
3aa: GLYCEROL (GOLaa)
3ab: GLYCEROL (GOLab)
3ac: GLYCEROL (GOLac)
3ad: GLYCEROL (GOLad)
3ae: GLYCEROL (GOLae)
3af: GLYCEROL (GOLaf)
3ag: GLYCEROL (GOLag)
3ah: GLYCEROL (GOLah)
3ai: GLYCEROL (GOLai)
3aj: GLYCEROL (GOLaj)
3ak: GLYCEROL (GOLak)
3al: GLYCEROL (GOLal)
3am: GLYCEROL (GOLam)
3an: GLYCEROL (GOLan)
3ao: GLYCEROL (GOLao)
3ap: GLYCEROL (GOLap)
3aq: GLYCEROL (GOLaq)
3ar: GLYCEROL (GOLar)
3as: GLYCEROL (GOLas)
3at: GLYCEROL (GOLat)
3au: GLYCEROL (GOLau)
3av: GLYCEROL (GOLav)
3aw: GLYCEROL (GOLaw)
3ax: GLYCEROL (GOLax)
3ay: GLYCEROL (GOLay)
3az: GLYCEROL (GOLaz)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
3r: GLYCEROL (GOLr)
3s: GLYCEROL (GOLs)
3t: GLYCEROL (GOLt)
3u: GLYCEROL (GOLu)
3v: GLYCEROL (GOLv)
3w: GLYCEROL (GOLw)
3x: GLYCEROL (GOLx)
3y: GLYCEROL (GOLy)
3z: GLYCEROL (GOLz)
4a: HYDROGEN PEROXIDE (PEOa)
4b: HYDROGEN PEROXIDE (PEOb)
4c: HYDROGEN PEROXIDE (PEOc)
4d: HYDROGEN PEROXIDE (PEOd)
4e: HYDROGEN PEROXIDE (PEOe)
4f: HYDROGEN PEROXIDE (PEOf)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
6a: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYa)
6b: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYb)
6c: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYc)
6d: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYd)
6e: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYe)
6f: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
6
Ligand/Ion
COPPER (II) ION
2
FOR
3
Mod. Residue
FORMYL GROUP
3
GOL
52
Ligand/Ion
GLYCEROL
4
PEO
6
Ligand/Ion
HYDROGEN PEROXIDE
5
PO4
3
Ligand/Ion
PHOSPHATE ION
6
TYY
6
Mod. Amino Acid
3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHEXA-1,4-DIENYL)-ALANINE
[
close Hetero Component info
]
Sites
(70, 70)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
59: GC5 (SOFTWARE)
60: GC6 (SOFTWARE)
61: GC7 (SOFTWARE)
62: GC8 (SOFTWARE)
63: GC9 (SOFTWARE)
64: HC1 (SOFTWARE)
65: HC2 (SOFTWARE)
66: HC3 (SOFTWARE)
67: HC4 (SOFTWARE)
68: HC5 (SOFTWARE)
69: HC6 (SOFTWARE)
70: HC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:456 , HIS A:458 , HIS A:624 , PEO A:802
BINDING SITE FOR RESIDUE CU A 801
02
AC2
SOFTWARE
TYY A:405 , LEU A:429 , HIS A:456 , HIS A:458 , HIS A:624 , MET A:634 , CU A:801 , HOH A:1055
BINDING SITE FOR RESIDUE PEO A 802
03
AC3
SOFTWARE
TRP A:156 , ASP A:319 , TYR A:323 , TYY A:405
BINDING SITE FOR RESIDUE FOR A 803
04
AC4
SOFTWARE
GLN A:66 , GLN A:70 , GLY A:72 , HOH A:955 , HOH A:1353 , TYR F:534 , GLU F:651
BINDING SITE FOR RESIDUE GOL A 804
05
AC5
SOFTWARE
LYS A:214 , VAL A:215 , GLY A:435 , ASP A:436 , ASN A:450 , HOH A:1133
BINDING SITE FOR RESIDUE GOL A 805
06
AC6
SOFTWARE
GLU A:368 , LYS A:393 , TYR A:410 , ASP A:422 , ARG A:424 , HOH A:1072 , HOH A:1542 , GLY B:371
BINDING SITE FOR RESIDUE GOL A 806
07
AC7
SOFTWARE
PRO A:484 , TYR A:485 , HOH A:1636
BINDING SITE FOR RESIDUE GOL A 807
08
AC8
SOFTWARE
HIS A:218 , LYS A:219 , TYR A:448 , HOH A:1185
BINDING SITE FOR RESIDUE GOL A 808
09
AC9
SOFTWARE
TYR A:160 , LYS A:561 , SER A:591 , HOH A:1246 , LYS F:561 , ASP F:593 , GOL F:811 , HOH F:994
BINDING SITE FOR RESIDUE GOL A 809
10
BC1
SOFTWARE
GLU A:110 , HOH A:1149 , HOH A:1509 , ALA F:133 , ILE F:204 , ILE F:206
BINDING SITE FOR RESIDUE GOL A 810
11
BC2
SOFTWARE
LYS A:68 , HOH F:1601
BINDING SITE FOR RESIDUE GOL A 811
12
BC3
SOFTWARE
GLY A:142 , PRO A:144 , GLU A:147 , TYR A:177 , HOH A:1624 , HOH E:1357
BINDING SITE FOR RESIDUE GOL A 812
13
BC4
SOFTWARE
ARG A:61 , ILE A:65 , ASP A:471 , ASP A:613 , HOH A:1327 , HOH A:1610
BINDING SITE FOR RESIDUE GOL A 813
14
BC5
SOFTWARE
ASP A:131 , ALA A:133 , VAL A:203 , ILE A:204 , HOH A:1645 , GLU F:110 , HOH F:1432
BINDING SITE FOR RESIDUE GOL A 814
15
BC6
SOFTWARE
PRO A:59 , ARG A:61 , HIS A:294 , TYR A:575 , ASN A:578 , HOH A:911 , HOH A:1141 , HOH A:1305 , HOH A:1406
BINDING SITE FOR RESIDUE GOL A 815
16
BC7
SOFTWARE
SER A:251 , LYS A:253 , GLU A:260 , TRP A:261 , SER A:262 , HOH A:1192 , HOH A:1257
BINDING SITE FOR RESIDUE GOL A 816
17
BC8
SOFTWARE
HIS B:456 , HIS B:458 , HIS B:624 , PEO B:802
BINDING SITE FOR RESIDUE CU B 801
18
BC9
SOFTWARE
TYY B:405 , LEU B:429 , HIS B:456 , HIS B:458 , HIS B:624 , MET B:634 , CU B:801 , HOH B:1094
BINDING SITE FOR RESIDUE PEO B 802
19
CC1
SOFTWARE
TRP B:156 , TYR B:323 , TYY B:405
BINDING SITE FOR RESIDUE FOR B 803
20
CC2
SOFTWARE
GLY A:371 , GLU B:368 , LYS B:393 , VAL B:412 , ASP B:422 , HOH B:1028 , HOH B:1472 , HOH B:1496
BINDING SITE FOR RESIDUE GOL B 804
21
CC3
SOFTWARE
GLU B:58 , PRO B:59 , HIS B:294 , TYR B:575 , ASN B:578 , HOH B:907 , HOH B:1037 , HOH B:1049 , HOH B:1285
BINDING SITE FOR RESIDUE GOL B 805
22
CC4
SOFTWARE
PRO B:484 , TYR B:499 , HOH B:1630
BINDING SITE FOR RESIDUE GOL B 806
23
CC5
SOFTWARE
TYR A:534 , HIS B:218 , LYS B:219 , TYR B:448 , PRO B:449 , PO4 B:812 , HOH B:1593
BINDING SITE FOR RESIDUE GOL B 807
24
CC6
SOFTWARE
LEU B:558 , LYS B:561 , SER B:591 , GOL B:809 , HOH B:988 , HOH B:1394 , LYS C:561 , ASP C:593
BINDING SITE FOR RESIDUE GOL B 808
25
CC7
SOFTWARE
LYS B:561 , ASP B:593 , GOL B:808 , HOH B:988 , HOH B:1487 , TYR C:160 , LYS C:561 , SER C:591 , HOH C:1512
BINDING SITE FOR RESIDUE GOL B 809
26
CC8
SOFTWARE
ARG B:61 , ILE B:65 , ASP B:471 , ASP B:613 , HOH B:1592
BINDING SITE FOR RESIDUE GOL B 810
27
CC9
SOFTWARE
ARG B:213 , LYS B:214 , VAL B:215 , ASP B:436 , ASN B:450 , HOH B:1021 , HOH B:1617
BINDING SITE FOR RESIDUE GOL B 811
28
DC1
SOFTWARE
HIS B:218 , LYS B:219 , GOL B:807
BINDING SITE FOR RESIDUE PO4 B 812
29
DC2
SOFTWARE
PRO B:144 , GLU B:147 , TYR B:177 , HOH B:1146 , HOH D:1410
BINDING SITE FOR RESIDUE GOL B 813
30
DC3
SOFTWARE
HIS C:456 , HIS C:458 , HIS C:624 , PEO C:802 , HOH C:1426
BINDING SITE FOR RESIDUE CU C 801
31
DC4
SOFTWARE
TYY C:405 , HIS C:456 , HIS C:458 , HIS C:624 , MET C:634 , CU C:801 , HOH C:990 , HOH C:1426
BINDING SITE FOR RESIDUE PEO C 802
32
DC5
SOFTWARE
HIS C:23 , TYR C:64 , LYS C:68 , ASP C:280 , HOH C:964 , HOH C:1521
BINDING SITE FOR RESIDUE GOL C 803
33
DC6
SOFTWARE
LYS C:214 , VAL C:215 , ASP C:436 , HOH C:1116 , HOH C:1256
BINDING SITE FOR RESIDUE GOL C 804
34
DC7
SOFTWARE
LYS B:68
BINDING SITE FOR RESIDUE GOL C 805
35
DC8
SOFTWARE
LYS C:393 , VAL C:412 , ASP C:422 , HOH C:1033 , HOH C:1562
BINDING SITE FOR RESIDUE GOL C 806
36
DC9
SOFTWARE
TYR C:499 , PRO D:442
BINDING SITE FOR RESIDUE GOL C 807
37
EC1
SOFTWARE
HIS C:218 , LYS C:219
BINDING SITE FOR RESIDUE PO4 C 808
38
EC2
SOFTWARE
GLN B:66 , GLN B:70 , GLY B:72 , TYR C:534 , GLU C:651 , HOH C:942 , HOH C:1487 , LYS D:231
BINDING SITE FOR RESIDUE GOL C 809
39
EC3
SOFTWARE
ARG C:57 , TYR C:80 , ASN C:578 , TYR C:581 , ASP C:585 , HOH C:1146 , HOH C:1262 , HOH C:1363 , HOH C:1495
BINDING SITE FOR RESIDUE GOL C 810
40
EC4
SOFTWARE
TYY D:405 , LEU D:429 , HIS D:456 , HIS D:458 , HIS D:624 , MET D:634 , CU D:703 , HOH D:805
BINDING SITE FOR RESIDUE PEO D 701
41
EC5
SOFTWARE
TRP D:156 , ASP D:319 , TYR D:323 , TYY D:405
BINDING SITE FOR RESIDUE FOR D 702
42
EC6
SOFTWARE
HIS D:456 , HIS D:458 , HIS D:624 , PEO D:701 , HOH D:1351
BINDING SITE FOR RESIDUE CU D 703
43
EC7
SOFTWARE
GLY D:142 , PRO D:144 , GLU D:147 , TYR D:177 , LYS D:217 , HOH D:1127 , HOH D:1466
BINDING SITE FOR RESIDUE GOL D 704
44
EC8
SOFTWARE
LYS D:150
BINDING SITE FOR RESIDUE GOL D 705
45
EC9
SOFTWARE
TYR D:499
BINDING SITE FOR RESIDUE GOL D 706
46
FC1
SOFTWARE
LYS B:62 , ALA B:63 , GLN B:66 , PRO B:73 , HOH B:1007 , HOH B:1345 , HOH B:1581 , LYS D:231 , VAL D:232 , GLY D:233
BINDING SITE FOR RESIDUE GOL D 707
47
FC2
SOFTWARE
GLU D:368 , LYS D:393 , VAL D:412 , ASP D:422 , ARG D:424 , HOH D:998 , HOH D:1429
BINDING SITE FOR RESIDUE GOL D 708
48
FC3
SOFTWARE
HIS D:23 , TYR D:64 , LYS D:68 , LYS D:265 , ASP D:280 , HOH D:909
BINDING SITE FOR RESIDUE GOL D 709
49
FC4
SOFTWARE
TRP D:67 , LYS D:68
BINDING SITE FOR RESIDUE GOL D 710
50
FC5
SOFTWARE
LEU D:56 , ARG D:57 , TYR D:80 , LEU D:580 , HOH D:993 , HOH D:1089 , HOH D:1487
BINDING SITE FOR RESIDUE GOL D 711
51
FC6
SOFTWARE
PHE D:252 , LYS D:253 , MET D:254 , ILE D:342 , HIS D:343
BINDING SITE FOR RESIDUE GOL D 712
52
FC7
SOFTWARE
HIS E:456 , HIS E:458 , HIS E:624 , PEO E:802 , HOH E:1432
BINDING SITE FOR RESIDUE CU E 801
53
FC8
SOFTWARE
TYY E:405 , LEU E:429 , HIS E:456 , HIS E:458 , HIS E:624 , MET E:634 , CU E:801 , HOH E:903
BINDING SITE FOR RESIDUE PEO E 802
54
FC9
SOFTWARE
GLY E:142 , PRO E:144 , GLU E:147 , TYR E:177 , LYS E:217 , HOH E:1248
BINDING SITE FOR RESIDUE GOL E 803
55
GC1
SOFTWARE
PHE E:252 , LYS E:253 , MET E:254 , ILE E:342 , HIS E:343 , HOH E:1486
BINDING SITE FOR RESIDUE GOL E 804
56
GC2
SOFTWARE
GLU E:58 , PRO E:59 , ARG E:295 , TYR E:575 , ASP E:577 , ASN E:578 , HOH E:948 , HOH E:957 , HOH E:1477 , HOH E:1502
BINDING SITE FOR RESIDUE GOL E 805
57
GC3
SOFTWARE
HIS E:23 , TYR E:64 , LYS E:68 , LYS E:265 , ASP E:280
BINDING SITE FOR RESIDUE GOL E 806
58
GC4
SOFTWARE
GLU E:368 , LYS E:393 , ARG E:420 , ASP E:422 , ARG E:424 , HOH E:1036 , HOH E:1308 , HOH E:1441 , GLY F:371
BINDING SITE FOR RESIDUE GOL E 807
59
GC5
SOFTWARE
HIS F:456 , HIS F:458 , HIS F:624 , PEO F:802 , HOH F:1395
BINDING SITE FOR RESIDUE CU F 801
60
GC6
SOFTWARE
TYY F:405 , HIS F:456 , HIS F:458 , HIS F:624 , MET F:634 , CU F:801 , HOH F:983 , HOH F:1395
BINDING SITE FOR RESIDUE PEO F 802
61
GC7
SOFTWARE
HIS F:23 , TYR F:64 , LYS F:68 , LYS F:265 , ASP F:280 , HOH F:946
BINDING SITE FOR RESIDUE GOL F 803
62
GC8
SOFTWARE
GLY E:371 , LYS F:393 , VAL F:412 , ASP F:422 , ARG F:424 , GOL F:805 , HOH F:1036 , HOH F:1525
BINDING SITE FOR RESIDUE GOL F 804
63
GC9
SOFTWARE
GLY E:371 , ARG E:390 , CYS F:338 , LYS F:339 , HIS F:366 , GLU F:368 , GOL F:804 , HOH F:1334
BINDING SITE FOR RESIDUE GOL F 805
64
HC1
SOFTWARE
PRO E:484 , PRO F:442
BINDING SITE FOR RESIDUE GOL F 806
65
HC2
SOFTWARE
PHE F:252 , LYS F:253 , MET F:254 , HIS F:343 , HOH F:1203
BINDING SITE FOR RESIDUE GOL F 807
66
HC3
SOFTWARE
PRO F:484
BINDING SITE FOR RESIDUE GOL F 808
67
HC4
SOFTWARE
HIS F:218 , LYS F:219 , HOH F:1528
BINDING SITE FOR RESIDUE PO4 F 809
68
HC5
SOFTWARE
LEU F:512 , ASP F:604 , GLY F:605 , HOH F:1069 , HOH F:1375 , HOH F:1596
BINDING SITE FOR RESIDUE GOL F 810
69
HC6
SOFTWARE
LYS A:561 , ASP A:593 , GOL A:809 , TYR F:160 , LEU F:558 , LYS F:561 , SER F:591 , HOH F:994 , HOH F:1489
BINDING SITE FOR RESIDUE GOL F 811
70
HC7
SOFTWARE
GLU F:58 , PRO F:59 , TYR F:575 , ASN F:578 , HOH F:924 , HOH F:987 , HOH F:1182
BINDING SITE FOR RESIDUE GOL F 812
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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Label:
End label:
Sorry, no Info available
[
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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
(0, 0)
Info
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[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
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Info
all PFAM domains
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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
Asymmetric Unit 1
Rendering
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by Chain (Biol. Unit)
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(e.g.: "#3cb371" or "60,179,113")
Stereo
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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)
[
close Script example commands
]
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") .
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