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4KFD
Asym. Unit
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (446 KB)
Biol.Unit 2 (450 KB)
Biol.Unit 3 (449 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HANSENULA POLYMORPHA COPPER AMINE OXIDASE-1 REDUCED BY METHYLAMINE AT PH 6.0
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
:
1.69
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
(5, 73)
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: GLYCEROL (GOLa)
2aa: GLYCEROL (GOLaa)
2ab: GLYCEROL (GOLab)
2ac: GLYCEROL (GOLac)
2ad: GLYCEROL (GOLad)
2ae: GLYCEROL (GOLae)
2af: GLYCEROL (GOLaf)
2ag: GLYCEROL (GOLag)
2ah: GLYCEROL (GOLah)
2ai: GLYCEROL (GOLai)
2aj: GLYCEROL (GOLaj)
2ak: GLYCEROL (GOLak)
2al: GLYCEROL (GOLal)
2am: GLYCEROL (GOLam)
2an: GLYCEROL (GOLan)
2ao: GLYCEROL (GOLao)
2ap: GLYCEROL (GOLap)
2aq: GLYCEROL (GOLaq)
2ar: GLYCEROL (GOLar)
2as: GLYCEROL (GOLas)
2at: GLYCEROL (GOLat)
2au: GLYCEROL (GOLau)
2av: GLYCEROL (GOLav)
2aw: GLYCEROL (GOLaw)
2ax: GLYCEROL (GOLax)
2ay: GLYCEROL (GOLay)
2az: GLYCEROL (GOLaz)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
2z: GLYCEROL (GOLz)
3a: HYDROGEN PEROXIDE (PEOa)
3b: HYDROGEN PEROXIDE (PEOb)
3c: HYDROGEN PEROXIDE (PEOc)
3d: HYDROGEN PEROXIDE (PEOd)
3e: HYDROGEN PEROXIDE (PEOe)
3f: HYDROGEN PEROXIDE (PEOf)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
5a: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYa)
5b: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYb)
5c: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYc)
5d: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYd)
5e: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYe)
5f: 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
GOL
52
Ligand/Ion
GLYCEROL
3
PEO
6
Ligand/Ion
HYDROGEN PEROXIDE
4
PO4
3
Ligand/Ion
PHOSPHATE ION
5
TYY
6
Mod. Amino Acid
3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHEXA-1,4-DIENYL)-ALANINE
[
close Hetero Component info
]
Sites
(66, 66)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:456 , HIS A:458 , HIS A:624 , PEO A:802 , HOH A:1428
BINDING SITE FOR RESIDUE CU A 801
02
AC2
SOFTWARE
TYY A:405 , HIS A:456 , HIS A:624 , MET A:634 , CU A:801 , HOH A:1052 , HOH A:1428
BINDING SITE FOR RESIDUE PEO A 802
03
AC3
SOFTWARE
GLN A:66 , GLN A:70 , GLY A:72 , HOH A:954 , HOH A:1348 , TYR F:534 , THR F:650
BINDING SITE FOR RESIDUE GOL A 803
04
AC4
SOFTWARE
LYS A:214 , VAL A:215 , GLY A:435 , ASP A:436 , HOH A:1131
BINDING SITE FOR RESIDUE GOL A 804
05
AC5
SOFTWARE
GLU A:368 , LYS A:393 , VAL A:412 , ASP A:422 , HOH A:1069 , HOH A:1561 , HOH A:1579 , GLY B:371
BINDING SITE FOR RESIDUE GOL A 805
06
AC6
SOFTWARE
PRO A:484 , HOH A:1690 , PRO B:442
BINDING SITE FOR RESIDUE GOL A 806
07
AC7
SOFTWARE
HIS A:218 , LYS A:219 , TYR A:448
BINDING SITE FOR RESIDUE GOL A 807
08
AC8
SOFTWARE
LYS A:561 , SER A:591 , HOH A:1245 , LYS F:561 , ASP F:593 , GOL F:811 , HOH F:996
BINDING SITE FOR RESIDUE GOL A 808
09
AC9
SOFTWARE
TRP A:67 , LYS A:68 , HOH F:1636
BINDING SITE FOR RESIDUE GOL A 809
10
BC1
SOFTWARE
GLY A:142 , PRO A:144 , GLU A:147 , TYR A:177 , HOH A:1678 , HOH E:1355
BINDING SITE FOR RESIDUE GOL A 810
11
BC2
SOFTWARE
ARG A:61 , LYS A:62 , ILE A:65 , ASP A:471 , ASP A:613 , HOH A:1323 , HOH A:1533 , HOH A:1663
BINDING SITE FOR RESIDUE GOL A 811
12
BC3
SOFTWARE
ASP A:131 , VAL A:203 , ILE A:204 , HOH A:1495 , HOH A:1698 , GLU F:110
BINDING SITE FOR RESIDUE GOL A 812
13
BC4
SOFTWARE
PRO A:59 , ARG A:61 , HIS A:294 , TYR A:575 , ASN A:578 , HOH A:911 , HOH A:1139 , HOH A:1302 , HOH A:1407
BINDING SITE FOR RESIDUE GOL A 813
14
BC5
SOFTWARE
SER A:251 , LYS A:253 , GLU A:260 , HOH A:1191 , HOH A:1255
BINDING SITE FOR RESIDUE GOL A 814
15
BC6
SOFTWARE
HIS B:456 , HIS B:458 , HIS B:624 , PEO B:802
BINDING SITE FOR RESIDUE CU B 801
16
BC7
SOFTWARE
TYY B:405 , LEU B:429 , HIS B:456 , HIS B:458 , HIS B:624 , MET B:634 , CU B:801 , HOH B:1096
BINDING SITE FOR RESIDUE PEO B 802
17
BC8
SOFTWARE
GLY A:371 , GLU B:368 , LYS B:393 , VAL B:412 , ARG B:420 , ASP B:422 , HOH B:1031 , HOH B:1527
BINDING SITE FOR RESIDUE GOL B 803
18
BC9
SOFTWARE
PRO B:59 , ALA B:60 , ARG B:61 , HIS B:294 , TYR B:575 , ASN B:578 , HOH B:908 , HOH B:1039 , HOH B:1051 , HOH B:1287
BINDING SITE FOR RESIDUE GOL B 804
19
CC1
SOFTWARE
PRO A:442 , PRO B:484 , TYR B:499
BINDING SITE FOR RESIDUE GOL B 805
20
CC2
SOFTWARE
TYR A:534 , HIS B:218 , LYS B:219 , TYR B:448 , PO4 B:810 , HOH B:1636
BINDING SITE FOR RESIDUE GOL B 806
21
CC3
SOFTWARE
LYS B:561 , SER B:591 , HOH B:990 , HOH B:1399 , LYS C:561 , ASP C:593 , GOL C:811
BINDING SITE FOR RESIDUE GOL B 807
22
CC4
SOFTWARE
ARG B:61 , ASP B:613 , HOH B:1516 , HOH B:1635 , HOH D:1396
BINDING SITE FOR RESIDUE GOL B 808
23
CC5
SOFTWARE
LYS B:214 , VAL B:215 , ASP B:436 , ASN B:450 , HOH B:1023 , HOH B:1659
BINDING SITE FOR RESIDUE GOL B 809
24
CC6
SOFTWARE
HIS B:218 , LYS B:219 , GOL B:806
BINDING SITE FOR RESIDUE PO4 B 810
25
CC7
SOFTWARE
GLY B:142 , PRO B:144 , GLU B:147 , TYR B:177 , VAL B:215 , HOH B:1147 , HOH D:1545
BINDING SITE FOR RESIDUE GOL B 811
26
CC8
SOFTWARE
HIS C:456 , HIS C:458 , HIS C:624 , PEO C:802 , HOH C:1427
BINDING SITE FOR RESIDUE CU C 801
27
CC9
SOFTWARE
TYY C:405 , HIS C:456 , HIS C:458 , HIS C:624 , MET C:634 , CU C:801 , HOH C:990 , HOH C:1427
BINDING SITE FOR RESIDUE PEO C 802
28
DC1
SOFTWARE
HIS C:23 , TYR C:64 , LYS C:68 , LYS C:265 , ASP C:280 , HOH C:965 , HOH C:1543
BINDING SITE FOR RESIDUE GOL C 803
29
DC2
SOFTWARE
LYS C:214 , VAL C:215 , GLY C:435 , ASP C:436 , HOH C:1252
BINDING SITE FOR RESIDUE GOL C 804
30
DC3
SOFTWARE
LYS B:68 , HOH C:1556
BINDING SITE FOR RESIDUE GOL C 805
31
DC4
SOFTWARE
GLU C:368 , LYS C:393 , VAL C:412 , ARG C:420 , ASP C:422 , HOH C:1034 , HOH C:1590 , GLY D:371
BINDING SITE FOR RESIDUE GOL C 806
32
DC5
SOFTWARE
PRO C:484 , TYR C:499 , PRO D:442
BINDING SITE FOR RESIDUE GOL C 807
33
DC6
SOFTWARE
HIS C:218 , LYS C:219
BINDING SITE FOR RESIDUE PO4 C 808
34
DC7
SOFTWARE
GLN B:66 , GLN B:70 , GLY B:72 , TYR C:534 , THR C:650 , GLU C:651 , HOH C:942 , HOH C:1509 , LYS D:231
BINDING SITE FOR RESIDUE GOL C 809
35
DC8
SOFTWARE
ARG C:57 , TYR C:80 , ASN C:578 , TYR C:581 , ASP C:585 , HOH C:1146 , HOH C:1257 , HOH C:1361 , HOH C:1412 , HOH C:1516
BINDING SITE FOR RESIDUE GOL C 810
36
DC9
SOFTWARE
LYS B:561 , ASP B:593 , GOL B:807 , HOH B:990 , TYR C:160 , LYS C:561 , SER C:591 , HOH C:1535
BINDING SITE FOR RESIDUE GOL C 811
37
EC1
SOFTWARE
HIS D:456 , HIS D:458 , HIS D:624 , PEO D:802 , HOH D:1473
BINDING SITE FOR RESIDUE CU D 801
38
EC2
SOFTWARE
TYY D:405 , HIS D:456 , HIS D:458 , HIS D:624 , MET D:634 , CU D:801 , HOH D:905
BINDING SITE FOR RESIDUE PEO D 802
39
EC3
SOFTWARE
GLY D:142 , PRO D:144 , GLU D:147 , TYR D:177 , LYS D:217 , GOL D:804 , HOH D:1226 , HOH D:1608
BINDING SITE FOR RESIDUE GOL D 803
40
EC4
SOFTWARE
LYS D:150 , TYR D:177 , GOL D:803 , HOH D:1322 , HOH D:1529
BINDING SITE FOR RESIDUE GOL D 804
41
EC5
SOFTWARE
LYS B:62 , ALA B:63 , GLN B:66 , PRO B:73 , HOH B:1010 , HOH B:1348 , HOH B:1625 , LYS D:231 , VAL D:232 , GLY D:233
BINDING SITE FOR RESIDUE GOL D 806
42
EC6
SOFTWARE
GLY C:371 , GLU D:368 , LYS D:393 , VAL D:412 , ARG D:420 , ASP D:422 , ARG D:424 , HOH D:1095 , HOH D:1275 , HOH D:1541 , HOH D:1570
BINDING SITE FOR RESIDUE GOL D 807
43
EC7
SOFTWARE
PRO D:18 , ALA D:19 , ALA D:99
BINDING SITE FOR RESIDUE GOL D 808
44
EC8
SOFTWARE
HIS D:23 , TYR D:64 , LYS D:68 , LYS D:265 , ASP D:280 , HOH D:1006
BINDING SITE FOR RESIDUE GOL D 809
45
EC9
SOFTWARE
TRP D:67 , LYS D:68
BINDING SITE FOR RESIDUE GOL D 810
46
FC1
SOFTWARE
LEU D:56 , ARG D:57 , TYR D:80 , LEU D:580 , HOH D:1090 , HOH D:1187 , HOH D:1634
BINDING SITE FOR RESIDUE GOL D 811
47
FC2
SOFTWARE
HIS E:456 , HIS E:458 , HIS E:624 , PEO E:802 , HOH E:1439
BINDING SITE FOR RESIDUE CU E 801
48
FC3
SOFTWARE
TYY E:405 , HIS E:456 , HIS E:458 , HIS E:624 , MET E:634 , CU E:801 , HOH E:903 , HOH E:1439
BINDING SITE FOR RESIDUE PEO E 802
49
FC4
SOFTWARE
GLY E:142 , PRO E:144 , GLU E:147 , TYR E:177 , LYS E:217 , HOH E:1249
BINDING SITE FOR RESIDUE GOL E 803
50
FC5
SOFTWARE
PHE E:252 , LYS E:253 , MET E:254 , ILE E:342 , HIS E:343 , HOH E:1507 , HOH E:1656
BINDING SITE FOR RESIDUE GOL E 804
51
FC6
SOFTWARE
GLU E:58 , PRO E:59 , TYR E:575 , ASP E:577 , ASN E:578 , HOH E:947 , HOH E:1524
BINDING SITE FOR RESIDUE GOL E 805
52
FC7
SOFTWARE
PRO E:484 , PRO F:442
BINDING SITE FOR RESIDUE GOL E 806
53
FC8
SOFTWARE
HIS E:23 , TYR E:64 , LYS E:68 , LYS E:265 , ASP E:280 , HOH E:975
BINDING SITE FOR RESIDUE GOL E 807
54
FC9
SOFTWARE
GLU E:368 , LYS E:393 , ARG E:420 , ASP E:422 , ARG E:424 , HOH E:1036 , HOH E:1307 , HOH E:1450 , GLY F:371
BINDING SITE FOR RESIDUE GOL E 808
55
GC1
SOFTWARE
HIS F:456 , HIS F:458 , HIS F:624 , PEO F:802 , HOH F:1402
BINDING SITE FOR RESIDUE CU F 801
56
GC2
SOFTWARE
TYY F:405 , LEU F:429 , HIS F:456 , HIS F:458 , HIS F:624 , MET F:634 , CU F:801 , HOH F:986
BINDING SITE FOR RESIDUE PEO F 802
57
GC3
SOFTWARE
HIS F:23 , TYR F:64 , LYS F:68 , LYS F:265 , ASP F:280 , HOH F:948 , HOH F:1470
BINDING SITE FOR RESIDUE GOL F 803
58
GC4
SOFTWARE
GLY E:371 , LYS F:393 , VAL F:412 , ARG F:420 , ASP F:422 , GOL F:805 , HOH F:1039
BINDING SITE FOR RESIDUE GOL F 804
59
GC5
SOFTWARE
GLY E:371 , ARG E:390 , ASP F:337 , CYS F:338 , LYS F:339 , GLU F:368 , GOL F:804 , HOH F:1338
BINDING SITE FOR RESIDUE GOL F 805
60
GC6
SOFTWARE
PHE F:252 , LYS F:253 , MET F:254 , HIS F:343 , HOH F:1202 , HOH F:1530
BINDING SITE FOR RESIDUE GOL F 806
61
GC7
SOFTWARE
PRO F:484 , TYR F:485 , TYR F:499
BINDING SITE FOR RESIDUE GOL F 807
62
GC8
SOFTWARE
HIS F:218 , LYS F:219
BINDING SITE FOR RESIDUE PO4 F 808
63
GC9
SOFTWARE
LEU F:512 , ASP F:604 , GLY F:605 , HOH F:1072 , HOH F:1382 , HOH F:1566 , HOH F:1628
BINDING SITE FOR RESIDUE GOL F 809
64
HC1
SOFTWARE
GLU A:110 , ALA F:133 , VAL F:203 , ILE F:204 , HOH F:1113 , HOH F:1409 , HOH F:1477 , HOH F:1629
BINDING SITE FOR RESIDUE GOL F 810
65
HC2
SOFTWARE
LYS A:561 , ASP A:593 , GOL A:808 , TYR F:160 , LYS F:561 , SER F:591 , HOH F:996 , HOH F:1517
BINDING SITE FOR RESIDUE GOL F 811
66
HC3
SOFTWARE
GLU F:58 , PRO F:59 , ARG F:61 , TYR F:575 , ASP F:577 , ASN F:578 , HOH F:925 , HOH F:990 , HOH F:1181 , HOH F:1214
BINDING SITE FOR RESIDUE GOL F 812
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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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
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select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (1.3 MB)
Header - Asym.Unit
Biol.Unit 1 (446 KB)
Header - Biol.Unit 1
Biol.Unit 2 (450 KB)
Header - Biol.Unit 2
Biol.Unit 3 (449 KB)
Header - Biol.Unit 3
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