0.027972
0.000000
0.000000
0.000000
0.015576
0.000000
0.000000
0.000000
0.015184
0.00000
0.00000
0.00000
Zhu, G.
Liu, J.
Terzyan, S.
Zhai, P.
Li, G.
Zhang, X.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
35.750
64.200
65.860
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
C2 H6 O S
78.133
BETA-MERCAPTOETHANOL
non-polymer
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
C10 H16 N5 O14 P3
523.180
n
GUANOSINE-5'-TRIPHOSPHATE
non-polymer
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-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
Mg 2
24.305
MAGNESIUM ION
non-polymer
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
278
2452
2460
10.1074/jbc.M211042200
12433916
High Resolution Crystal Structures of Human Rab5a and Five Mutants with Substitutions in the Catalytically Important Phosphate-Binding Loop
2003
10.2210/pdb1n6l/pdb
pdb_00001n6l
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
IMAGE PLATE
2002-08-23
MARRESEARCH
OSMIC OPTICS
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
19013.609
Ras-related protein Rab-5A
GTPASE DOMAIN
A30P
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
523.180
GUANOSINE-5'-TRIPHOSPHATE
1
syn
non-polymer
78.133
BETA-MERCAPTOETHANOL
1
syn
non-polymer
18.015
water
254
nat
water
rab5a
no
no
GNKICQFKLVLLGESPVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQ
AAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIF
MAIAKKLPKN
GNKICQFKLVLLGESPVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQ
AAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIF
MAIAKKLPKN
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
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
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
human
Homo
Escherichia
Escherichia coli
sample
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
BL21(DE3)
PLASMID
pET11a
1
2
37.5
VAPOR DIFFUSION, HANGING DROP
6.0
PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-11-27
1
1
2008-04-28
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
rab5a wild type
rab5a A30P mutant complex with GDP
rab5a A30P mutant complex with GDP and aluminum fluoride
Rab5a A30R mutant complex with GppNHp
Rab5a A30K mutant complex with GppNHp
Rab5a A30E mutant complex with GppNHp
Rab5a A30L mutant complex with GppNHp
RCSB
Y
RCSB
2002-11-11
REL
REL
MG
MAGNESIUM ION
GTP
GUANOSINE-5'-TRIPHOSPHATE
BME
BETA-MERCAPTOETHANOL
HOH
water
MG2
201
2
MG
MG
201
A
GTP
200
3
GTP
GTP
200
A
BME
210
4
BME
BME
210
A
WAT
301
5
HOH
HOH
301
A
WAT
302
5
HOH
HOH
302
A
WAT
303
5
HOH
HOH
303
A
WAT
304
5
HOH
HOH
304
A
WAT
305
5
HOH
HOH
305
A
WAT
306
5
HOH
HOH
306
A
WAT
307
5
HOH
HOH
307
A
WAT
308
5
HOH
HOH
308
A
WAT
309
5
HOH
HOH
309
A
WAT
310
5
HOH
HOH
310
A
WAT
311
5
HOH
HOH
311
A
WAT
312
5
HOH
HOH
312
A
WAT
313
5
HOH
HOH
313
A
WAT
314
5
HOH
HOH
314
A
WAT
315
5
HOH
HOH
315
A
WAT
316
5
HOH
HOH
316
A
WAT
317
5
HOH
HOH
317
A
WAT
318
5
HOH
HOH
318
A
WAT
319
5
HOH
HOH
319
A
WAT
320
5
HOH
HOH
320
A
WAT
321
5
HOH
HOH
321
A
WAT
322
5
HOH
HOH
322
A
WAT
323
5
HOH
HOH
323
A
WAT
324
5
HOH
HOH
324
A
WAT
325
5
HOH
HOH
325
A
WAT
326
5
HOH
HOH
326
A
WAT
327
5
HOH
HOH
327
A
WAT
328
5
HOH
HOH
328
A
WAT
329
5
HOH
HOH
329
A
WAT
330
5
HOH
HOH
330
A
WAT
331
5
HOH
HOH
331
A
WAT
332
5
HOH
HOH
332
A
WAT
333
5
HOH
HOH
333
A
WAT
334
5
HOH
HOH
334
A
WAT
335
5
HOH
HOH
335
A
WAT
336
5
HOH
HOH
336
A
WAT
337
5
HOH
HOH
337
A
WAT
338
5
HOH
HOH
338
A
WAT
339
5
HOH
HOH
339
A
WAT
340
5
HOH
HOH
340
A
WAT
341
5
HOH
HOH
341
A
WAT
342
5
HOH
HOH
342
A
WAT
343
5
HOH
HOH
343
A
WAT
344
5
HOH
HOH
344
A
WAT
345
5
HOH
HOH
345
A
WAT
346
5
HOH
HOH
346
A
WAT
347
5
HOH
HOH
347
A
WAT
348
5
HOH
HOH
348
A
WAT
349
5
HOH
HOH
349
A
WAT
350
5
HOH
HOH
350
A
WAT
351
5
HOH
HOH
351
A
WAT
352
5
HOH
HOH
352
A
WAT
353
5
HOH
HOH
353
A
WAT
354
5
HOH
HOH
354
A
WAT
355
5
HOH
HOH
355
A
WAT
356
5
HOH
HOH
356
A
WAT
357
5
HOH
HOH
357
A
WAT
358
5
HOH
HOH
358
A
WAT
359
5
HOH
HOH
359
A
WAT
360
5
HOH
HOH
360
A
WAT
361
5
HOH
HOH
361
A
WAT
362
5
HOH
HOH
362
A
WAT
363
5
HOH
HOH
363
A
WAT
364
5
HOH
HOH
364
A
WAT
365
5
HOH
HOH
365
A
WAT
366
5
HOH
HOH
366
A
WAT
367
5
HOH
HOH
367
A
WAT
368
5
HOH
HOH
368
A
WAT
369
5
HOH
HOH
369
A
WAT
370
5
HOH
HOH
370
A
WAT
371
5
HOH
HOH
371
A
WAT
372
5
HOH
HOH
372
A
WAT
373
5
HOH
HOH
373
A
WAT
374
5
HOH
HOH
374
A
WAT
375
5
HOH
HOH
375
A
WAT
376
5
HOH
HOH
376
A
WAT
377
5
HOH
HOH
377
A
WAT
378
5
HOH
HOH
378
A
WAT
379
5
HOH
HOH
379
A
WAT
380
5
HOH
HOH
380
A
WAT
381
5
HOH
HOH
381
A
WAT
382
5
HOH
HOH
382
A
WAT
383
5
HOH
HOH
383
A
WAT
384
5
HOH
HOH
384
A
WAT
385
5
HOH
HOH
385
A
WAT
386
5
HOH
HOH
386
A
WAT
387
5
HOH
HOH
387
A
WAT
388
5
HOH
HOH
388
A
WAT
389
5
HOH
HOH
389
A
WAT
390
5
HOH
HOH
390
A
WAT
391
5
HOH
HOH
391
A
WAT
392
5
HOH
HOH
392
A
WAT
393
5
HOH
HOH
393
A
WAT
394
5
HOH
HOH
394
A
WAT
395
5
HOH
HOH
395
A
WAT
396
5
HOH
HOH
396
A
WAT
397
5
HOH
HOH
397
A
WAT
398
5
HOH
HOH
398
A
WAT
399
5
HOH
HOH
399
A
WAT
400
5
HOH
HOH
400
A
WAT
401
5
HOH
HOH
401
A
WAT
402
5
HOH
HOH
402
A
WAT
403
5
HOH
HOH
403
A
WAT
404
5
HOH
HOH
404
A
WAT
405
5
HOH
HOH
405
A
WAT
406
5
HOH
HOH
406
A
WAT
407
5
HOH
HOH
407
A
WAT
408
5
HOH
HOH
408
A
WAT
409
5
HOH
HOH
409
A
WAT
410
5
HOH
HOH
410
A
WAT
411
5
HOH
HOH
411
A
WAT
412
5
HOH
HOH
412
A
WAT
413
5
HOH
HOH
413
A
WAT
414
5
HOH
HOH
414
A
WAT
415
5
HOH
HOH
415
A
WAT
416
5
HOH
HOH
416
A
WAT
417
5
HOH
HOH
417
A
WAT
418
5
HOH
HOH
418
A
WAT
419
5
HOH
HOH
419
A
WAT
420
5
HOH
HOH
420
A
WAT
421
5
HOH
HOH
421
A
WAT
422
5
HOH
HOH
422
A
WAT
423
5
HOH
HOH
423
A
WAT
424
5
HOH
HOH
424
A
WAT
425
5
HOH
HOH
425
A
WAT
426
5
HOH
HOH
426
A
WAT
427
5
HOH
HOH
427
A
WAT
428
5
HOH
HOH
428
A
WAT
429
5
HOH
HOH
429
A
WAT
430
5
HOH
HOH
430
A
WAT
431
5
HOH
HOH
431
A
WAT
432
5
HOH
HOH
432
A
WAT
433
5
HOH
HOH
433
A
WAT
434
5
HOH
HOH
434
A
WAT
435
5
HOH
HOH
435
A
WAT
436
5
HOH
HOH
436
A
WAT
437
5
HOH
HOH
437
A
WAT
438
5
HOH
HOH
438
A
WAT
439
5
HOH
HOH
439
A
WAT
440
5
HOH
HOH
440
A
WAT
441
5
HOH
HOH
441
A
WAT
442
5
HOH
HOH
442
A
WAT
443
5
HOH
HOH
443
A
WAT
444
5
HOH
HOH
444
A
WAT
445
5
HOH
HOH
445
A
WAT
446
5
HOH
HOH
446
A
WAT
447
5
HOH
HOH
447
A
WAT
448
5
HOH
HOH
448
A
WAT
449
5
HOH
HOH
449
A
WAT
450
5
HOH
HOH
450
A
WAT
451
5
HOH
HOH
451
A
WAT
452
5
HOH
HOH
452
A
WAT
453
5
HOH
HOH
453
A
WAT
454
5
HOH
HOH
454
A
WAT
455
5
HOH
HOH
455
A
WAT
456
5
HOH
HOH
456
A
WAT
457
5
HOH
HOH
457
A
WAT
458
5
HOH
HOH
458
A
WAT
459
5
HOH
HOH
459
A
WAT
460
5
HOH
HOH
460
A
WAT
461
5
HOH
HOH
461
A
WAT
462
5
HOH
HOH
462
A
WAT
463
5
HOH
HOH
463
A
WAT
464
5
HOH
HOH
464
A
WAT
465
5
HOH
HOH
465
A
WAT
466
5
HOH
HOH
466
A
WAT
467
5
HOH
HOH
467
A
WAT
468
5
HOH
HOH
468
A
WAT
469
5
HOH
HOH
469
A
WAT
470
5
HOH
HOH
470
A
WAT
471
5
HOH
HOH
471
A
WAT
472
5
HOH
HOH
472
A
WAT
473
5
HOH
HOH
473
A
WAT
474
5
HOH
HOH
474
A
WAT
475
5
HOH
HOH
475
A
WAT
476
5
HOH
HOH
476
A
WAT
477
5
HOH
HOH
477
A
WAT
478
5
HOH
HOH
478
A
WAT
479
5
HOH
HOH
479
A
WAT
480
5
HOH
HOH
480
A
WAT
481
5
HOH
HOH
481
A
WAT
482
5
HOH
HOH
482
A
WAT
483
5
HOH
HOH
483
A
WAT
484
5
HOH
HOH
484
A
WAT
485
5
HOH
HOH
485
A
WAT
486
5
HOH
HOH
486
A
WAT
487
5
HOH
HOH
487
A
WAT
488
5
HOH
HOH
488
A
WAT
489
5
HOH
HOH
489
A
WAT
490
5
HOH
HOH
490
A
WAT
491
5
HOH
HOH
491
A
WAT
492
5
HOH
HOH
492
A
WAT
493
5
HOH
HOH
493
A
WAT
494
5
HOH
HOH
494
A
WAT
495
5
HOH
HOH
495
A
WAT
496
5
HOH
HOH
496
A
WAT
497
5
HOH
HOH
497
A
WAT
498
5
HOH
HOH
498
A
WAT
499
5
HOH
HOH
499
A
WAT
500
5
HOH
HOH
500
A
WAT
501
5
HOH
HOH
501
A
WAT
502
5
HOH
HOH
502
A
WAT
503
5
HOH
HOH
503
A
WAT
504
5
HOH
HOH
504
A
WAT
505
5
HOH
HOH
505
A
WAT
506
5
HOH
HOH
506
A
WAT
507
5
HOH
HOH
507
A
WAT
508
5
HOH
HOH
508
A
WAT
509
5
HOH
HOH
509
A
WAT
510
5
HOH
HOH
510
A
WAT
511
5
HOH
HOH
511
A
WAT
512
5
HOH
HOH
512
A
WAT
513
5
HOH
HOH
513
A
WAT
514
5
HOH
HOH
514
A
WAT
515
5
HOH
HOH
515
A
WAT
516
5
HOH
HOH
516
A
WAT
517
5
HOH
HOH
517
A
WAT
518
5
HOH
HOH
518
A
WAT
519
5
HOH
HOH
519
A
WAT
520
5
HOH
HOH
520
A
WAT
521
5
HOH
HOH
521
A
WAT
522
5
HOH
HOH
522
A
WAT
523
5
HOH
HOH
523
A
WAT
524
5
HOH
HOH
524
A
WAT
525
5
HOH
HOH
525
A
WAT
526
5
HOH
HOH
526
A
WAT
527
5
HOH
HOH
527
A
WAT
528
5
HOH
HOH
528
A
WAT
529
5
HOH
HOH
529
A
WAT
530
5
HOH
HOH
530
A
WAT
531
5
HOH
HOH
531
A
WAT
532
5
HOH
HOH
532
A
WAT
533
5
HOH
HOH
533
A
WAT
534
5
HOH
HOH
534
A
WAT
535
5
HOH
HOH
535
A
WAT
536
5
HOH
HOH
536
A
WAT
537
5
HOH
HOH
537
A
WAT
538
5
HOH
HOH
538
A
WAT
539
5
HOH
HOH
539
A
WAT
540
5
HOH
HOH
540
A
WAT
541
5
HOH
HOH
541
A
WAT
542
5
HOH
HOH
542
A
WAT
543
5
HOH
HOH
543
A
WAT
544
5
HOH
HOH
544
A
WAT
545
5
HOH
HOH
545
A
WAT
546
5
HOH
HOH
546
A
WAT
547
5
HOH
HOH
547
A
WAT
548
5
HOH
HOH
548
A
WAT
549
5
HOH
HOH
549
A
WAT
550
5
HOH
HOH
550
A
WAT
551
5
HOH
HOH
551
A
WAT
552
5
HOH
HOH
552
A
WAT
553
5
HOH
HOH
553
A
WAT
554
5
HOH
HOH
554
A
GLY
15
n
1
GLY
15
A
ASN
16
n
2
ASN
16
A
LYS
17
n
3
LYS
17
A
ILE
18
n
4
ILE
18
A
CYS
19
n
5
CYS
19
A
GLN
20
n
6
GLN
20
A
PHE
21
n
7
PHE
21
A
LYS
22
n
8
LYS
22
A
LEU
23
n
9
LEU
23
A
VAL
24
n
10
VAL
24
A
LEU
25
n
11
LEU
25
A
LEU
26
n
12
LEU
26
A
GLY
27
n
13
GLY
27
A
GLU
28
n
14
GLU
28
A
SER
29
n
15
SER
29
A
PRO
30
n
16
PRO
30
A
VAL
31
n
17
VAL
31
A
GLY
32
n
18
GLY
32
A
LYS
33
n
19
LYS
33
A
SER
34
n
20
SER
34
A
SER
35
n
21
SER
35
A
LEU
36
n
22
LEU
36
A
VAL
37
n
23
VAL
37
A
LEU
38
n
24
LEU
38
A
ARG
39
n
25
ARG
39
A
PHE
40
n
26
PHE
40
A
VAL
41
n
27
VAL
41
A
LYS
42
n
28
LYS
42
A
GLY
43
n
29
GLY
43
A
GLN
44
n
30
GLN
44
A
PHE
45
n
31
PHE
45
A
HIS
46
n
32
HIS
46
A
GLU
47
n
33
GLU
47
A
PHE
48
n
34
PHE
48
A
GLN
49
n
35
GLN
49
A
GLU
50
n
36
GLU
50
A
SER
51
n
37
SER
51
A
THR
52
n
38
THR
52
A
ILE
53
n
39
ILE
53
A
GLY
54
n
40
GLY
54
A
ALA
55
n
41
ALA
55
A
ALA
56
n
42
ALA
56
A
PHE
57
n
43
PHE
57
A
LEU
58
n
44
LEU
58
A
THR
59
n
45
THR
59
A
GLN
60
n
46
GLN
60
A
THR
61
n
47
THR
61
A
VAL
62
n
48
VAL
62
A
CYS
63
n
49
CYS
63
A
LEU
64
n
50
LEU
64
A
ASP
65
n
51
ASP
65
A
ASP
66
n
52
ASP
66
A
THR
67
n
53
THR
67
A
THR
68
n
54
THR
68
A
VAL
69
n
55
VAL
69
A
LYS
70
n
56
LYS
70
A
PHE
71
n
57
PHE
71
A
GLU
72
n
58
GLU
72
A
ILE
73
n
59
ILE
73
A
TRP
74
n
60
TRP
74
A
ASP
75
n
61
ASP
75
A
THR
76
n
62
THR
76
A
ALA
77
n
63
ALA
77
A
GLY
78
n
64
GLY
78
A
GLN
79
n
65
GLN
79
A
GLU
80
n
66
GLU
80
A
ARG
81
n
67
ARG
81
A
TYR
82
n
68
TYR
82
A
HIS
83
n
69
HIS
83
A
SER
84
n
70
SER
84
A
LEU
85
n
71
LEU
85
A
ALA
86
n
72
ALA
86
A
PRO
87
n
73
PRO
87
A
MET
88
n
74
MET
88
A
TYR
89
n
75
TYR
89
A
TYR
90
n
76
TYR
90
A
ARG
91
n
77
ARG
91
A
GLY
92
n
78
GLY
92
A
ALA
93
n
79
ALA
93
A
GLN
94
n
80
GLN
94
A
ALA
95
n
81
ALA
95
A
ALA
96
n
82
ALA
96
A
ILE
97
n
83
ILE
97
A
VAL
98
n
84
VAL
98
A
VAL
99
n
85
VAL
99
A
TYR
100
n
86
TYR
100
A
ASP
101
n
87
ASP
101
A
ILE
102
n
88
ILE
102
A
THR
103
n
89
THR
103
A
ASN
104
n
90
ASN
104
A
GLU
105
n
91
GLU
105
A
GLU
106
n
92
GLU
106
A
SER
107
n
93
SER
107
A
PHE
108
n
94
PHE
108
A
ALA
109
n
95
ALA
109
A
ARG
110
n
96
ARG
110
A
ALA
111
n
97
ALA
111
A
LYS
112
n
98
LYS
112
A
ASN
113
n
99
ASN
113
A
TRP
114
n
100
TRP
114
A
VAL
115
n
101
VAL
115
A
LYS
116
n
102
LYS
116
A
GLU
117
n
103
GLU
117
A
LEU
118
n
104
LEU
118
A
GLN
119
n
105
GLN
119
A
ARG
120
n
106
ARG
120
A
GLN
121
n
107
GLN
121
A
ALA
122
n
108
ALA
122
A
SER
123
n
109
SER
123
A
PRO
124
n
110
PRO
124
A
ASN
125
n
111
ASN
125
A
ILE
126
n
112
ILE
126
A
VAL
127
n
113
VAL
127
A
ILE
128
n
114
ILE
128
A
ALA
129
n
115
ALA
129
A
LEU
130
n
116
LEU
130
A
SER
131
n
117
SER
131
A
GLY
132
n
118
GLY
132
A
ASN
133
n
119
ASN
133
A
LYS
134
n
120
LYS
134
A
ALA
135
n
121
ALA
135
A
ASP
136
n
122
ASP
136
A
LEU
137
n
123
LEU
137
A
ALA
138
n
124
ALA
138
A
ASN
139
n
125
ASN
139
A
LYS
140
n
126
LYS
140
A
ARG
141
n
127
ARG
141
A
ALA
142
n
128
ALA
142
A
VAL
143
n
129
VAL
143
A
ASP
144
n
130
ASP
144
A
PHE
145
n
131
PHE
145
A
GLN
146
n
132
GLN
146
A
GLU
147
n
133
GLU
147
A
ALA
148
n
134
ALA
148
A
GLN
149
n
135
GLN
149
A
SER
150
n
136
SER
150
A
TYR
151
n
137
TYR
151
A
ALA
152
n
138
ALA
152
A
ASP
153
n
139
ASP
153
A
ASP
154
n
140
ASP
154
A
ASN
155
n
141
ASN
155
A
SER
156
n
142
SER
156
A
LEU
157
n
143
LEU
157
A
LEU
158
n
144
LEU
158
A
PHE
159
n
145
PHE
159
A
MET
160
n
146
MET
160
A
GLU
161
n
147
GLU
161
A
THR
162
n
148
THR
162
A
SER
163
n
149
SER
163
A
ALA
164
n
150
ALA
164
A
LYS
165
n
151
LYS
165
A
THR
166
n
152
THR
166
A
SER
167
n
153
SER
167
A
MET
168
n
154
MET
168
A
ASN
169
n
155
ASN
169
A
VAL
170
n
156
VAL
170
A
ASN
171
n
157
ASN
171
A
GLU
172
n
158
GLU
172
A
ILE
173
n
159
ILE
173
A
PHE
174
n
160
PHE
174
A
MET
175
n
161
MET
175
A
ALA
176
n
162
ALA
176
A
ILE
177
n
163
ILE
177
A
ALA
178
n
164
ALA
178
A
LYS
179
n
165
LYS
179
A
LYS
180
n
166
LYS
180
A
LEU
181
n
167
LEU
181
A
PRO
182
n
168
PRO
182
A
n
169
183
A
n
170
184
A
author_defined_assembly
1
monomeric
A
SER
34
A
OG
SER
20
1_555
A
MG
201
B
MG
MG
1_555
A
THR
52
A
OG1
THR
38
1_555
85.2
A
SER
34
A
OG
SER
20
1_555
A
MG
201
B
MG
MG
1_555
A
GTP
200
C
O2G
GTP
1_555
175.3
A
THR
52
A
OG1
THR
38
1_555
A
MG
201
B
MG
MG
1_555
A
GTP
200
C
O2G
GTP
1_555
90.1
A
SER
34
A
OG
SER
20
1_555
A
MG
201
B
MG
MG
1_555
A
GTP
200
C
O2B
GTP
1_555
91.7
A
THR
52
A
OG1
THR
38
1_555
A
MG
201
B
MG
MG
1_555
A
GTP
200
C
O2B
GTP
1_555
176.0
A
GTP
200
C
O2G
GTP
1_555
A
MG
201
B
MG
MG
1_555
A
GTP
200
C
O2B
GTP
1_555
92.9
A
SER
34
A
OG
SER
20
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
301
E
O
HOH
1_555
86.5
A
THR
52
A
OG1
THR
38
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
301
E
O
HOH
1_555
92.1
A
GTP
200
C
O2G
GTP
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
301
E
O
HOH
1_555
94.5
A
GTP
200
C
O2B
GTP
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
301
E
O
HOH
1_555
90.3
A
SER
34
A
OG
SER
20
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
302
E
O
HOH
1_555
87.0
A
THR
52
A
OG1
THR
38
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
302
E
O
HOH
1_555
88.6
A
GTP
200
C
O2G
GTP
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
302
E
O
HOH
1_555
92.0
A
GTP
200
C
O2B
GTP
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
302
E
O
HOH
1_555
88.7
A
HOH
301
E
O
HOH
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
302
E
O
HOH
1_555
173.4
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
N
GLN
60
A
N
GLN
46
A
O
PHE
71
A
O
PHE
57
A
O
THR
68
A
O
THR
54
A
N
LYS
17
A
N
LYS
3
A
N
LEU
26
A
N
LEU
12
A
O
VAL
99
A
O
VAL
85
A
N
VAL
98
A
N
VAL
84
A
O
ALA
129
A
O
ALA
115
A
N
LEU
130
A
N
LEU
116
A
O
LEU
158
A
O
LEU
144
1
A
LYS
183
A
LYS
169
1
Y
1
A
ASN
184
A
ASN
170
1
Y
1
A
PRO
30
-119.49
76.99
1
A
ASP
65
63.71
-110.65
1
A
LEU
137
-98.95
34.65
1
A
SER
167
97.88
-2.62
1
A
ASN
169
58.15
12.67
protein_rep.param
protein.top
gtp.param
gtp.top
water_rep.param
water.top
ion.param
ion.top
bme1.param
bme1.top
1.938
0
0
-1.332
0
-0.606
0.211
0.173
0.18
0.18
1.60
20
19501
20631
20496
99.2
RANDOM
1
THROUGHOUT
0.0
FOURIER SYNTHESIS
Engh & Huber
0.20
0.16
5
0.12
0.06
1.60
20
254
1633
37
0
1342
0.010
1.48
1.808
1.5
2.504
2
3.199
2
4.406
2.5
18.1
1.60
20
1N6L
20631
20496
0.0
0.0
0.042
1
41.1
7.6
99.3
0.13
1.60
1.66
15.9
98.8
data reduction
DENZO
data scaling
SCALEPACK
refinement
CNS
phasing
CNS
Crystal Structure of Human Rab5a A30P mutant complex with GTP
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
A
GLY
32
A
GLY
18
HELX_P
A
GLY
43
A
GLY
29
1
1
12
A
GLN
79
A
GLN
65
HELX_P
A
SER
84
A
SER
70
5
2
6
A
LEU
85
A
LEU
71
HELX_P
A
ARG
91
A
ARG
77
1
3
7
A
ASN
104
A
ASN
90
HELX_P
A
ALA
122
A
ALA
108
1
4
19
A
LYS
134
A
LYS
120
HELX_P
A
ARG
141
A
ARG
127
5
5
8
A
ASP
144
A
ASP
130
HELX_P
A
ASN
155
A
ASN
141
1
6
12
A
ASN
169
A
ASN
155
HELX_P
A
LEU
181
A
LEU
167
1
7
13
covale
2.035
none
A
CYS
63
A
SG
CYS
49
1_555
A
BME
210
D
S2
BME
1_555
metalc
2.123
A
SER
34
A
OG
SER
20
1_555
A
MG
201
B
MG
MG
1_555
metalc
2.123
A
THR
52
A
OG1
THR
38
1_555
A
MG
201
B
MG
MG
1_555
metalc
2.020
A
GTP
200
C
O2G
GTP
1_555
A
MG
201
B
MG
MG
1_555
metalc
2.065
A
GTP
200
C
O2B
GTP
1_555
A
MG
201
B
MG
MG
1_555
metalc
2.120
A
MG
201
B
MG
MG
1_555
A
HOH
301
E
O
HOH
1_555
metalc
2.131
A
MG
201
B
MG
MG
1_555
A
HOH
302
E
O
HOH
1_555
PROTEIN TRANSPORT
Rab, GTPase, protein transport
A
SER
29
A
SER
15
1
A
PRO
30
A
PRO
16
-0.19
RAB5A_HUMAN
UNP
1
15
P20339
GNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQ
AAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIF
MAIAKKLPKN
15
184
1N6L
15
184
P20339
A
1
1
170
1
ALA
engineered mutation
PRO
30
1N6L
A
P20339
UNP
30
16
6
anti-parallel
parallel
parallel
parallel
parallel
A
ALA
55
A
ALA
41
A
LEU
64
A
LEU
50
A
THR
67
A
THR
53
A
THR
76
A
THR
62
A
LYS
17
A
LYS
3
A
GLY
27
A
GLY
13
A
ALA
95
A
ALA
81
A
ASP
101
A
ASP
87
A
VAL
127
A
VAL
113
A
ASN
133
A
ASN
119
A
LEU
158
A
LEU
144
A
GLU
161
A
GLU
147
BINDING SITE FOR RESIDUE MG A 201
A
MG
201
Software
5
BINDING SITE FOR RESIDUE GTP A 200
A
GTP
200
Software
30
BINDING SITE FOR RESIDUE BME A 210
A
BME
210
Software
7
A
SER
34
A
SER
20
5
1_555
A
THR
52
A
THR
38
5
1_555
A
GTP
200
C
GTP
5
1_555
A
HOH
301
E
HOH
5
1_555
A
HOH
302
E
HOH
5
1_555
A
SER
29
A
SER
15
30
1_555
A
PRO
30
A
PRO
16
30
1_555
A
VAL
31
A
VAL
17
30
1_555
A
GLY
32
A
GLY
18
30
1_555
A
LYS
33
A
LYS
19
30
1_555
A
SER
34
A
SER
20
30
1_555
A
SER
35
A
SER
21
30
1_555
A
PHE
45
A
PHE
31
30
1_555
A
HIS
46
A
HIS
32
30
1_555
A
GLU
47
A
GLU
33
30
1_555
A
GLN
49
A
GLN
35
30
1_555
A
THR
52
A
THR
38
30
1_555
A
GLY
78
A
GLY
64
30
1_555
A
ASN
133
A
ASN
119
30
1_555
A
LYS
134
A
LYS
120
30
1_555
A
ASP
136
A
ASP
122
30
1_555
A
LEU
137
A
LEU
123
30
1_555
A
SER
163
A
SER
149
30
1_555
A
ALA
164
A
ALA
150
30
1_555
A
LYS
165
A
LYS
151
30
1_555
A
LYS
180
A
LYS
166
30
2_555
A
MG
201
B
MG
30
1_555
A
HOH
301
E
HOH
30
1_555
A
HOH
302
E
HOH
30
1_555
A
HOH
303
E
HOH
30
1_555
A
HOH
304
E
HOH
30
1_555
A
HOH
333
E
HOH
30
1_555
A
HOH
341
E
HOH
30
1_555
A
HOH
400
E
HOH
30
1_555
A
HOH
474
E
HOH
30
1_555
A
GLY
15
A
GLY
1
7
1_555
A
ALA
55
A
ALA
41
7
4_556
A
CYS
63
A
CYS
49
7
1_555
A
ASP
65
A
ASP
51
7
1_555
A
ASP
66
A
ASP
52
7
1_555
A
THR
67
A
THR
53
7
1_555
A
THR
68
A
THR
54
7
1_555
19
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