0.014187
0.008191
0.000000
0.000000
0.016382
0.000000
0.000000
0.000000
0.016291
0.00000
0.00000
0.00000
Prag, G.
Misra, S.
Jones, E.
Ghirlando, R.
Davies, B.A.
Horazdovsky, B.F.
Hurley, J.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
70.487
70.487
61.384
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Cell(Cambridge,Mass.)
CELLB5
0998
0092-8674
113
609
620
10.1016/S0092-8674(03)00364-7
12787502
Mechanism of Ubiquitin Recognition by the CUE Domain of Vps9p
2003
10.2210/pdb1mn3/pdb
pdb_00001mn3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
95.0
1
CCD
2002-07-13
SBC-2
Sagitally focused Si(111)
MAD
M
x-ray
1
0.95645
1.0
0.97910
1.0
0.97924
1.0
19-ID
APS
0.95645,0.97910,0.97924
SYNCHROTRON
APS BEAMLINE 19-ID
6222.829
Vacuolar protein sorting-associated protein VPS9
Cue domain (residues 398-451)
G440E
1
man
polymer
18.015
water
31
nat
water
no
yes
SSLIKKIEENERKDTLNTLQN(MSE)FPD(MSE)DPSLIEDVCIAKKSRIEPCVDALLSLSE
SSLIKKIEENERKDTLNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLSLSE
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
baker's yeast
Saccharomyces
Escherichia
sample
VPS9
4932
Saccharomyces cerevisiae
562
Escherichia coli
BL21(DE3)-Rosetta
PLASMID
pHis-parallel2
1
3.54
65.21
The number of unique reflections observed include
Friedel pairs
VAPOR DIFFUSION, HANGING DROP
8.5
Ammonium Sulfate, Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
database_2
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Database references
Derived calculations
1
0
2003-06-10
1
1
2008-04-28
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2002-09-04
REL
REL
HOH
water
WAT
1
2
HOH
HOH
1
A
WAT
2
2
HOH
HOH
2
A
WAT
3
2
HOH
HOH
3
A
WAT
4
2
HOH
HOH
4
A
WAT
5
2
HOH
HOH
5
A
WAT
6
2
HOH
HOH
6
A
WAT
8
2
HOH
HOH
8
A
WAT
9
2
HOH
HOH
9
A
WAT
10
2
HOH
HOH
10
A
WAT
11
2
HOH
HOH
11
A
WAT
12
2
HOH
HOH
12
A
WAT
13
2
HOH
HOH
13
A
WAT
14
2
HOH
HOH
14
A
WAT
15
2
HOH
HOH
15
A
WAT
16
2
HOH
HOH
16
A
WAT
17
2
HOH
HOH
17
A
WAT
18
2
HOH
HOH
18
A
WAT
19
2
HOH
HOH
19
A
WAT
20
2
HOH
HOH
20
A
WAT
21
2
HOH
HOH
21
A
WAT
22
2
HOH
HOH
22
A
WAT
23
2
HOH
HOH
23
A
WAT
24
2
HOH
HOH
24
A
WAT
25
2
HOH
HOH
25
A
WAT
26
2
HOH
HOH
26
A
WAT
27
2
HOH
HOH
27
A
WAT
28
2
HOH
HOH
28
A
WAT
29
2
HOH
HOH
29
A
WAT
30
2
HOH
HOH
30
A
WAT
31
2
HOH
HOH
31
A
WAT
32
2
HOH
HOH
32
A
SER
398
n
1
SER
398
A
SER
399
n
2
SER
399
A
LEU
400
n
3
LEU
400
A
ILE
401
n
4
ILE
401
A
LYS
402
n
5
LYS
402
A
LYS
403
n
6
LYS
403
A
ILE
404
n
7
ILE
404
A
GLU
405
n
8
GLU
405
A
GLU
406
n
9
GLU
406
A
ASN
407
n
10
ASN
407
A
GLU
408
n
11
GLU
408
A
ARG
409
n
12
ARG
409
A
LYS
410
n
13
LYS
410
A
ASP
411
n
14
ASP
411
A
THR
412
n
15
THR
412
A
LEU
413
n
16
LEU
413
A
ASN
414
n
17
ASN
414
A
THR
415
n
18
THR
415
A
LEU
416
n
19
LEU
416
A
GLN
417
n
20
GLN
417
A
ASN
418
n
21
ASN
418
A
MSE
419
n
22
MSE
419
A
PHE
420
n
23
PHE
420
A
PRO
421
n
24
PRO
421
A
ASP
422
n
25
ASP
422
A
MSE
423
n
26
MSE
423
A
ASP
424
n
27
ASP
424
A
PRO
425
n
28
PRO
425
A
SER
426
n
29
SER
426
A
LEU
427
n
30
LEU
427
A
ILE
428
n
31
ILE
428
A
GLU
429
n
32
GLU
429
A
ASP
430
n
33
ASP
430
A
VAL
431
n
34
VAL
431
A
CYS
432
n
35
CYS
432
A
ILE
433
n
36
ILE
433
A
ALA
434
n
37
ALA
434
A
LYS
435
n
38
LYS
435
A
LYS
436
n
39
LYS
436
A
SER
437
n
40
SER
437
A
ARG
438
n
41
ARG
438
A
ILE
439
n
42
ILE
439
A
GLU
440
n
43
GLU
440
A
PRO
441
n
44
PRO
441
A
CYS
442
n
45
CYS
442
A
VAL
443
n
46
VAL
443
A
ASP
444
n
47
ASP
444
A
ALA
445
n
48
ALA
445
A
LEU
446
n
49
LEU
446
A
LEU
447
n
50
LEU
447
A
SER
448
n
51
SER
448
A
LEU
449
n
52
LEU
449
A
SER
450
n
53
SER
450
A
GLU
451
n
54
GLU
451
A
author_defined_assembly
1
monomeric
software_defined_assembly
PISA,PQS
2
dimeric
1740
-22
7490
A
MSE
419
SELENOMETHIONINE
A
MSE
22
MET
A
MSE
423
SELENOMETHIONINE
A
MSE
26
MET
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
0.5000000000
0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
12_565
x,x-y+1,-z+5/6
crystal symmetry operation
-35.2435000000
61.0435326366
51.1533333333
1
A
A
O
O
HOH
HOH
19
19
1.21
1_555
9_555
1
A
A
O
O
HOH
HOH
29
29
1.40
1_555
10_666
1
A
A
O
O
HOH
HOH
10
10
1.66
1_555
12_565
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
42.2
0.34
5.75
0.00
0.34
0.00
-0.68
0.266
0.010
0.244
2.3
43.29
763
7562
7325
10.4
96.6
RANDOM
1
RESTRAINED
THROUGHOUT
0.0
MAD
Engh & Huber
FLAT MODEL
39.9679
0.3658
0.39
0.31
5.00
0.38
2.3
43.29
31
456
0
0
425
0.006
1.1
18.4
0.86
1.74
1.50
2.89
2.00
3.25
2.00
4.36
2.50
0.363
0.038
0.302
2.44
91
1043
1043
6
8.0
88.6
2.3
50.0
1MN3
7562
7325
-3.0
0.079
1
39.5
24.5
99.8
0.418
2.3
2.38
6.8
415
1
100.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
SOLVE
model building
RESOLVE
refinement
CNS
1.1
phasing
RESOLVE
Cue domain of yeast Vps9p
1
N
N
2
N
N
A
SER
398
A
SER
1
HELX_P
A
PHE
420
A
PHE
23
1
1
23
A
ASP
424
A
ASP
27
HELX_P
A
ILE
433
A
ILE
36
1
2
10
A
ARG
438
A
ARG
41
HELX_P
A
GLU
451
A
GLU
54
1
3
14
disulf
2.706
A
CYS
432
A
SG
CYS
35
1_555
A
CYS
442
A
SG
CYS
45
12_565
covale
1.330
both
A
ASN
418
A
C
ASN
21
1_555
A
MSE
419
A
N
MSE
22
1_555
covale
1.334
both
A
MSE
419
A
C
MSE
22
1_555
A
PHE
420
A
N
PHE
23
1_555
covale
1.327
both
A
ASP
422
A
C
ASP
25
1_555
A
MSE
423
A
N
MSE
26
1_555
covale
1.326
both
A
MSE
423
A
C
MSE
26
1_555
A
ASP
424
A
N
ASP
27
1_555
PROTEIN TRANSPORT
Ubiquitin, PROTEIN TRANSPORT
VPS9_YEAST
UNP
1
398
P54787
SSLIKKIEENERKDTLNTLQNMFPDMDPSLIEDVCIAKKSRIGPCVDALLSLSE
398
451
1MN3
398
451
P54787
A
1
1
54
1
MET
modified residue
MSE
419
1MN3
A
P54787
UNP
419
22
1
MET
modified residue
MSE
423
1MN3
A
P54787
UNP
423
26
1
GLY
engineered mutation
GLU
440
1MN3
A
P54787
UNP
440
43
179
P 65 2 2