1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Pires, J.R.
Hong, X.
Brockmann, C.
Volkmer-Engert, R.
Schneider-Mergener, J.
Oschkinat, H.
Erdmann, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
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
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
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
326
1427
1435
10.1016/S0022-2836(03)00039-1
12595255
The ScPex13p SH3 Domain Exposes Two Distinct Binding Sites for Pex5p and Pex14p
2003
10.2210/pdb1nm7/pdb
pdb_00001nm7
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
8086.208
Peroxisomal Membrane Protein PAS20
SH3 domain
1
man
polymer
Pex13p SH3 domain
no
no
GSHHHHHHFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEII
GSHHHHHHFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEII
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
baker's yeast
Saccharomyces
Escherichia
Escherichia coli
sample
4932
Saccharomyces cerevisiae
469008
Escherichia coli BL21(DE3)
BL21-DE3
plasmid
pGEX-4T2
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-03-04
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
1N5Z contains complex structure of PEX13P SH3 domain with a peptide of PEX14P
RCSB
Y
PDBJ
2003-01-09
REL
REL
structures with the lowest energy
100
10
3D_13C-separated_NOESY
3D_15N-separated_NOESY
2D NOESY
2D NOESY
50mM NaCl
6.0
1
atm
298
K
AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS AS IMPLEMENTED IN ARIA1.0
1
lowest energy
0.7mM [U-15N,13C] Pex13p SH3 domain, 20mM Phosphate Buffer, pH 6.0, 50mM NaCl
100% D2O
0.7mM [U-15N] Pex13p SH3 domain, 20mM Phosphate Buffer, pH 6.0, 50mM NaCl
90% H2O/10% D2O
0.7mM Unlabeled Pex13p SH3 domain, 20mM Phosphate Buffer, pH 6.0, 50mM NaCl
90% H2O/10% D2O
0.7mM Unlabeled Pex13p SH3 domain, 20mM Phosphate Buffer, pH 6.0, 50mM NaCl
100% D2O
Bruker
processing
XwinNMR
data analysis
Sparky
3.106
J.P.Linge, S.I.O'Donoghue, M.Nilges
structure solution
ARIA
1.0
structure solution
CNS
1.0
refinement
CNS
1.0
600
Bruker
DRX
n
1
302
A
n
2
303
A
n
3
304
A
n
4
305
A
n
5
306
A
n
6
307
A
n
7
308
A
n
8
309
A
PHE
310
n
9
PHE
310
A
ALA
311
n
10
ALA
311
A
ARG
312
n
11
ARG
312
A
ALA
313
n
12
ALA
313
A
LEU
314
n
13
LEU
314
A
TYR
315
n
14
TYR
315
A
ASP
316
n
15
ASP
316
A
PHE
317
n
16
PHE
317
A
VAL
318
n
17
VAL
318
A
PRO
319
n
18
PRO
319
A
GLU
320
n
19
GLU
320
A
ASN
321
n
20
ASN
321
A
PRO
322
n
21
PRO
322
A
GLU
323
n
22
GLU
323
A
MET
324
n
23
MET
324
A
GLU
325
n
24
GLU
325
A
VAL
326
n
25
VAL
326
A
ALA
327
n
26
ALA
327
A
LEU
328
n
27
LEU
328
A
LYS
329
n
28
LYS
329
A
LYS
330
n
29
LYS
330
A
GLY
331
n
30
GLY
331
A
ASP
332
n
31
ASP
332
A
LEU
333
n
32
LEU
333
A
MET
334
n
33
MET
334
A
ALA
335
n
34
ALA
335
A
ILE
336
n
35
ILE
336
A
LEU
337
n
36
LEU
337
A
SER
338
n
37
SER
338
A
LYS
339
n
38
LYS
339
A
LYS
340
n
39
LYS
340
A
ASP
341
n
40
ASP
341
A
PRO
342
n
41
PRO
342
A
LEU
343
n
42
LEU
343
A
GLY
344
n
43
GLY
344
A
ARG
345
n
44
ARG
345
A
ASP
346
n
45
ASP
346
A
SER
347
n
46
SER
347
A
ASP
348
n
47
ASP
348
A
TRP
349
n
48
TRP
349
A
TRP
350
n
49
TRP
350
A
LYS
351
n
50
LYS
351
A
VAL
352
n
51
VAL
352
A
ARG
353
n
52
ARG
353
A
THR
354
n
53
THR
354
A
LYS
355
n
54
LYS
355
A
ASN
356
n
55
ASN
356
A
GLY
357
n
56
GLY
357
A
ASN
358
n
57
ASN
358
A
ILE
359
n
58
ILE
359
A
GLY
360
n
59
GLY
360
A
TYR
361
n
60
TYR
361
A
ILE
362
n
61
ILE
362
A
PRO
363
n
62
PRO
363
A
TYR
364
n
63
TYR
364
A
ASN
365
n
64
ASN
365
A
TYR
366
n
65
TYR
366
A
ILE
367
n
66
ILE
367
A
GLU
368
n
67
GLU
368
A
ILE
369
n
68
ILE
369
A
ILE
370
n
69
ILE
370
A
author_defined_assembly
1
monomeric
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
A
O
ASN
358
A
O
ASN
57
A
N
THR
354
A
N
THR
53
A
O
ARG
353
A
O
ARG
52
A
N
ALA
335
A
N
ALA
34
A
O
MET
334
A
O
MET
33
A
N
ALA
311
A
N
ALA
10
A
N
ARG
312
A
N
ARG
11
A
O
GLU
368
A
O
GLU
67
1
A
GLY
302
A
GLY
1
1
Y
1
A
SER
303
A
SER
2
1
Y
1
A
HIS
304
A
HIS
3
1
Y
1
A
HIS
305
A
HIS
4
1
Y
1
A
HIS
306
A
HIS
5
1
Y
1
A
HIS
307
A
HIS
6
1
Y
1
A
HIS
308
A
HIS
7
1
Y
1
A
HIS
309
A
HIS
8
1
Y
2
A
GLY
302
A
GLY
1
1
Y
2
A
SER
303
A
SER
2
1
Y
2
A
HIS
304
A
HIS
3
1
Y
2
A
HIS
305
A
HIS
4
1
Y
2
A
HIS
306
A
HIS
5
1
Y
2
A
HIS
307
A
HIS
6
1
Y
2
A
HIS
308
A
HIS
7
1
Y
2
A
HIS
309
A
HIS
8
1
Y
3
A
GLY
302
A
GLY
1
1
Y
3
A
SER
303
A
SER
2
1
Y
3
A
HIS
304
A
HIS
3
1
Y
3
A
HIS
305
A
HIS
4
1
Y
3
A
HIS
306
A
HIS
5
1
Y
3
A
HIS
307
A
HIS
6
1
Y
3
A
HIS
308
A
HIS
7
1
Y
3
A
HIS
309
A
HIS
8
1
Y
4
A
GLY
302
A
GLY
1
1
Y
4
A
SER
303
A
SER
2
1
Y
4
A
HIS
304
A
HIS
3
1
Y
4
A
HIS
305
A
HIS
4
1
Y
4
A
HIS
306
A
HIS
5
1
Y
4
A
HIS
307
A
HIS
6
1
Y
4
A
HIS
308
A
HIS
7
1
Y
4
A
HIS
309
A
HIS
8
1
Y
5
A
GLY
302
A
GLY
1
1
Y
5
A
SER
303
A
SER
2
1
Y
5
A
HIS
304
A
HIS
3
1
Y
5
A
HIS
305
A
HIS
4
1
Y
5
A
HIS
306
A
HIS
5
1
Y
5
A
HIS
307
A
HIS
6
1
Y
5
A
HIS
308
A
HIS
7
1
Y
5
A
HIS
309
A
HIS
8
1
Y
6
A
GLY
302
A
GLY
1
1
Y
6
A
SER
303
A
SER
2
1
Y
6
A
HIS
304
A
HIS
3
1
Y
6
A
HIS
305
A
HIS
4
1
Y
6
A
HIS
306
A
HIS
5
1
Y
6
A
HIS
307
A
HIS
6
1
Y
6
A
HIS
308
A
HIS
7
1
Y
6
A
HIS
309
A
HIS
8
1
Y
7
A
GLY
302
A
GLY
1
1
Y
7
A
SER
303
A
SER
2
1
Y
7
A
HIS
304
A
HIS
3
1
Y
7
A
HIS
305
A
HIS
4
1
Y
7
A
HIS
306
A
HIS
5
1
Y
7
A
HIS
307
A
HIS
6
1
Y
7
A
HIS
308
A
HIS
7
1
Y
7
A
HIS
309
A
HIS
8
1
Y
8
A
GLY
302
A
GLY
1
1
Y
8
A
SER
303
A
SER
2
1
Y
8
A
HIS
304
A
HIS
3
1
Y
8
A
HIS
305
A
HIS
4
1
Y
8
A
HIS
306
A
HIS
5
1
Y
8
A
HIS
307
A
HIS
6
1
Y
8
A
HIS
308
A
HIS
7
1
Y
8
A
HIS
309
A
HIS
8
1
Y
9
A
GLY
302
A
GLY
1
1
Y
9
A
SER
303
A
SER
2
1
Y
9
A
HIS
304
A
HIS
3
1
Y
9
A
HIS
305
A
HIS
4
1
Y
9
A
HIS
306
A
HIS
5
1
Y
9
A
HIS
307
A
HIS
6
1
Y
9
A
HIS
308
A
HIS
7
1
Y
9
A
HIS
309
A
HIS
8
1
Y
10
A
GLY
302
A
GLY
1
1
Y
10
A
SER
303
A
SER
2
1
Y
10
A
HIS
304
A
HIS
3
1
Y
10
A
HIS
305
A
HIS
4
1
Y
10
A
HIS
306
A
HIS
5
1
Y
10
A
HIS
307
A
HIS
6
1
Y
10
A
HIS
308
A
HIS
7
1
Y
10
A
HIS
309
A
HIS
8
1
Y
1
A
A
HA
HB3
PRO
GLU
319
325
1.34
2
A
A
HB3
HB3
ASP
TYR
348
364
1.31
3
A
A
HB3
HB3
ASP
TYR
348
364
1.30
5
A
A
HB3
HG23
MET
VAL
334
352
1.33
6
A
A
HB3
HB3
ASP
TYR
348
364
1.32
7
A
A
HB3
HB3
ASP
TYR
348
364
1.32
10
A
A
HB3
HB3
ASP
TYR
348
364
1.26
10
A
A
HA
HB3
PRO
GLU
319
325
1.32
1
A
LEU
314
-76.06
-70.14
1
A
ASP
316
-54.04
105.85
1
A
PRO
319
-43.45
106.29
1
A
PRO
322
-75.04
40.86
1
A
GLU
323
-130.70
-43.75
1
A
MET
324
-164.57
102.12
1
A
LYS
330
-10.75
105.74
1
A
ASP
332
-58.53
-172.40
1
A
LEU
337
-121.88
-59.97
1
A
LYS
339
-126.63
-120.68
1
A
ASP
341
104.86
-63.49
1
A
PRO
342
-92.15
-77.09
1
A
ARG
345
-80.76
-154.15
1
A
SER
347
167.84
161.01
1
A
TRP
349
-167.56
104.55
1
A
ILE
362
-175.63
118.25
2
A
ASP
316
-47.84
107.67
2
A
PRO
319
-37.51
103.03
2
A
PRO
322
-74.82
37.90
2
A
GLU
323
-130.29
-39.35
2
A
MET
324
-165.88
101.74
2
A
LYS
330
-22.96
114.92
2
A
ASP
332
-56.49
176.14
2
A
LEU
337
-131.49
-43.79
2
A
LYS
339
-133.73
-117.57
2
A
ASP
341
109.39
-59.04
2
A
PRO
342
-85.40
-71.98
2
A
LEU
343
-91.08
-71.06
2
A
ARG
345
-77.85
-128.58
2
A
ASP
346
-100.93
-141.38
2
A
SER
347
65.95
150.45
2
A
TRP
349
-161.55
113.37
2
A
ILE
362
-178.92
121.63
3
A
ASP
316
-53.46
109.90
3
A
PRO
319
-38.02
103.11
3
A
PRO
322
-74.44
46.28
3
A
GLU
323
-133.01
-44.79
3
A
LYS
330
-24.02
129.74
3
A
ASP
332
-58.13
172.08
3
A
LYS
339
-132.12
-119.66
3
A
ASP
341
108.45
-60.81
3
A
LEU
343
-94.34
-75.43
3
A
ARG
345
-75.49
-123.17
3
A
ASP
346
-105.54
-144.35
3
A
SER
347
65.58
151.75
4
A
PRO
319
-38.70
103.67
4
A
PRO
322
-75.06
38.61
4
A
MET
324
-165.33
101.06
4
A
LYS
330
28.69
-96.95
4
A
LYS
339
-129.75
-117.17
4
A
ASP
341
108.25
-59.40
4
A
PRO
342
-89.28
-83.70
4
A
ARG
345
-79.29
-121.14
4
A
ASP
346
-108.67
-147.59
4
A
SER
347
67.53
151.37
4
A
ILE
362
-178.66
119.85
5
A
ASP
316
-53.22
108.55
5
A
PRO
319
-47.93
98.98
5
A
PRO
322
-74.39
39.83
5
A
GLU
323
-130.66
-38.26
5
A
MET
324
-162.17
101.20
5
A
LYS
330
-16.87
112.92
5
A
ASP
332
-61.31
-174.17
5
A
LEU
337
-130.57
-78.84
5
A
SER
338
-53.82
174.02
5
A
LYS
339
-129.18
-119.29
5
A
ASP
341
103.00
-64.23
5
A
PRO
342
-94.07
-82.77
5
A
ARG
345
-86.93
-150.61
5
A
SER
347
163.87
160.64
5
A
TRP
349
-167.20
112.97
5
A
LYS
355
48.32
26.00
5
A
ASN
365
174.19
-35.92
6
A
ASP
316
-50.21
107.59
6
A
PRO
319
-47.74
98.81
6
A
PRO
322
-75.40
40.88
6
A
GLU
323
-134.56
-40.60
6
A
MET
324
-160.25
100.46
6
A
LYS
330
25.08
-95.49
6
A
LYS
339
-123.26
-121.32
6
A
ASP
341
107.73
-61.72
6
A
PRO
342
-80.91
-75.98
6
A
ARG
345
-98.30
-126.15
6
A
SER
347
78.90
152.25
6
A
ILE
362
178.75
131.11
7
A
LEU
314
-72.69
-77.82
7
A
ASP
316
-53.35
105.44
7
A
PRO
319
-49.15
103.19
7
A
PRO
322
-75.05
42.50
7
A
GLU
323
-131.99
-35.09
7
A
MET
324
-165.27
100.30
7
A
LYS
330
-15.70
118.38
7
A
ASP
332
-59.83
-176.34
7
A
LEU
337
-121.84
-72.18
7
A
LYS
339
-117.97
-121.07
7
A
ASP
341
76.02
-178.66
7
A
PRO
342
-26.18
-46.74
7
A
ARG
345
-103.70
-156.20
7
A
SER
347
166.31
156.60
7
A
TRP
349
-165.13
107.75
7
A
LYS
355
49.35
21.08
7
A
ILE
362
-175.35
119.25
8
A
GLU
323
-137.24
-37.79
8
A
MET
324
-165.57
99.90
8
A
LYS
330
-16.57
118.45
8
A
LEU
337
-120.97
-69.96
8
A
LYS
339
-129.00
-114.39
8
A
ASP
341
93.18
-77.10
8
A
ARG
345
-68.63
-119.63
8
A
ASP
346
-120.62
-109.65
8
A
SER
347
56.58
158.83
8
A
TRP
349
-167.28
108.39
8
A
ILE
362
-171.51
118.55
8
A
ASN
365
-176.28
-41.07
9
A
ASP
316
-52.96
105.88
9
A
PRO
319
-38.67
100.97
9
A
PRO
322
-76.03
42.86
9
A
GLU
323
-131.92
-44.38
9
A
LYS
330
-13.46
121.15
9
A
LYS
339
-107.41
-136.16
9
A
ASP
341
103.62
-63.56
9
A
PRO
342
-96.02
-88.23
9
A
ARG
345
-69.59
-156.41
9
A
SER
347
-48.79
161.80
9
A
LYS
355
47.66
26.66
9
A
ILE
362
-174.80
122.02
9
A
ASN
365
173.02
-36.61
10
A
TYR
315
76.76
108.82
10
A
ASP
316
-39.70
114.05
10
A
PRO
319
-38.59
97.16
10
A
PRO
322
-75.58
40.59
10
A
GLU
323
-137.45
-41.50
10
A
MET
324
-161.19
101.46
10
A
LYS
330
-19.92
116.66
10
A
ASP
332
-58.46
173.21
10
A
LEU
337
-128.69
-74.35
10
A
LYS
339
-137.67
-116.74
10
A
ASP
341
115.41
-56.64
10
A
LEU
343
-111.02
-80.88
10
A
ARG
345
-92.65
-109.64
10
A
ASP
346
19.17
-139.58
10
A
LYS
355
49.35
21.47
10
A
ILE
362
-172.14
128.39
10
A
TYR
364
-63.22
91.55
10
A
ASN
365
-177.79
-34.15
Solution structure of the ScPex13p SH3 domain
1
N
N
A
PRO
363
A
PRO
62
HELX_P
A
ASN
365
A
ASN
64
5
1
3
PROTEIN TRANSPORT
Yeast, Membrane protein, Pex5p, Pex14p, Pex13p, import machine, SH3 domain, PROTEIN TRANSPORT
PEX13_YEAST
UNP
1
310
P80667
FARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEII
310
370
1NM7
310
370
P80667
A
1
9
69
1
expression tag
GLY
302
1NM7
A
P80667
UNP
1
1
expression tag
SER
303
1NM7
A
P80667
UNP
2
1
expression tag
HIS
304
1NM7
A
P80667
UNP
3
1
expression tag
HIS
305
1NM7
A
P80667
UNP
4
1
expression tag
HIS
306
1NM7
A
P80667
UNP
5
1
expression tag
HIS
307
1NM7
A
P80667
UNP
6
1
expression tag
HIS
308
1NM7
A
P80667
UNP
7
1
expression tag
HIS
309
1NM7
A
P80667
UNP
8
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ASN
358
A
ASN
57
A
ILE
362
A
ILE
61
A
TRP
350
A
TRP
49
A
THR
354
A
THR
53
A
LEU
333
A
LEU
32
A
ILE
336
A
ILE
35
A
ALA
311
A
ALA
10
A
ALA
313
A
ALA
12
A
ILE
367
A
ILE
66
A
ILE
369
A
ILE
68