0.025699
0.000000
0.004159
0.000000
0.022748
0.000000
0.000000
0.000000
0.012631
0.00000
0.00000
0.00000
Stogios, P.J.
Wawrzak, Z.
Evdokimova, E.
Minasov, G.
Egorova, O.
Di Leo, R.
Kudritska, M.
Yim, V.
Meziane-Cherif, D.
Courvalin, P.
Savchenko, A.
Anderson, W.F.
Center for Structural Genomics of Infectious Diseases (CSGID)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
99.19
90.00
38.912
43.960
80.199
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
Cl -1
35.453
CHLORIDE ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
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 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
O4 S -2
96.063
SULFATE ION
non-polymer
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
Zn 2
65.409
ZINC ION
non-polymer
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
111
5872
5877
10.1073/pnas.1402259111
24711382
Structural basis for the evolution of vancomycin resistance D,D-peptidases.
2014
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
mirrors
CCD
2011-07-09
MARMOSAIC 300 mm CCD
SI {1,1,1}
SINGLE WAVELENGTH
M
x-ray
1
0.97918
1.0
21-ID-D
APS
0.97918
SYNCHROTRON
APS BEAMLINE 21-ID-D
29775.939
D,D-dipeptidase/D,D-carboxypeptidase
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
35.453
CHLORIDE ION
1
syn
non-polymer
96.063
SULFATE ION
1
syn
non-polymer
62.068
1,2-ETHANEDIOL
10
syn
non-polymer
92.094
GLYCEROL
3
syn
non-polymer
18.015
water
187
nat
water
D,D-peptidase, VanXYG
no
yes
G(MSE)(MSE)KTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNIL(MSE)KRDVANVLQLIFEKISAGNSI
VPVSGYRSLEEQTAIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGF
TQRYARDKEEITGISHEPWHFRYVGYPHSKI(MSE)QENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDK
TLIKIPENCVYQISGNNIDGFVVTIWRKTDD
GMMKTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNILMKRDVANVLQLIFEKISAGNSIVPVSGYRSLEEQ
TAIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGFTQRYARDKEEIT
GISHEPWHFRYVGYPHSKIMQENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDKTLIKIPENCVYQISGN
NIDGFVVTIWRKTDD
A
IDP91774
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
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
BM4518
sample
vanXYG, vanYG2
1351
Enterococcus faecalis
469008
Escherichia coli
BL21(DE3)
plasmid
p15Tv lic
1
2.27
45.91
VAPOR DIFFUSION, SITTING DROP
6.3
0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% PEG 8K, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
Center for Structural Genomics of Infectious Diseases
CSGID
NIAID, National Institute of Allergy and Infectious Diseases
repository
Initial release
Structure summary
Structure summary
Other
Database references
Database references
1
0
2012-05-23
1
1
2013-10-02
1
2
2013-10-16
1
3
2014-01-22
1
4
2014-04-23
1
5
2014-05-14
Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog
Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant
Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Ala-D-Ala phosphinate analog
Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine
Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II)
Y
RCSB
Y
RCSB
2012-05-15
REL
REL
ZN
ZINC ION
CL
CHLORIDE ION
SO4
SULFATE ION
EDO
1,2-ETHANEDIOL
GOL
GLYCEROL
HOH
water
ZN
1
2
ZN
ZN
301
A
CL
2
3
CL
CL
302
A
SO4
3
4
SO4
SO4
303
A
EDO
9
5
EDO
EDO
304
A
EDO
10
5
EDO
EDO
305
A
EDO
11
5
EDO
EDO
306
A
EDO
12
5
EDO
EDO
307
A
EDO
13
5
EDO
EDO
308
A
EDO
14
5
EDO
EDO
309
A
EDO
15
5
EDO
EDO
310
A
EDO
16
5
EDO
EDO
311
A
EDO
17
5
EDO
EDO
312
A
EDO
18
5
EDO
EDO
313
A
GOL
19
6
GOL
GOL
314
A
GOL
20
6
GOL
GOL
315
A
GOL
21
6
GOL
GOL
316
A
HOH
2
7
HOH
HOH
401
A
HOH
3
7
HOH
HOH
402
A
HOH
4
7
HOH
HOH
403
A
HOH
5
7
HOH
HOH
404
A
HOH
6
7
HOH
HOH
405
A
HOH
7
7
HOH
HOH
406
A
HOH
8
7
HOH
HOH
407
A
HOH
9
7
HOH
HOH
408
A
HOH
10
7
HOH
HOH
409
A
HOH
11
7
HOH
HOH
410
A
HOH
12
7
HOH
HOH
411
A
HOH
13
7
HOH
HOH
412
A
HOH
14
7
HOH
HOH
413
A
HOH
15
7
HOH
HOH
414
A
HOH
16
7
HOH
HOH
415
A
HOH
17
7
HOH
HOH
416
A
HOH
18
7
HOH
HOH
417
A
HOH
19
7
HOH
HOH
418
A
HOH
20
7
HOH
HOH
419
A
HOH
21
7
HOH
HOH
420
A
HOH
23
7
HOH
HOH
421
A
HOH
24
7
HOH
HOH
422
A
HOH
25
7
HOH
HOH
423
A
HOH
26
7
HOH
HOH
424
A
HOH
27
7
HOH
HOH
425
A
HOH
28
7
HOH
HOH
426
A
HOH
29
7
HOH
HOH
427
A
HOH
30
7
HOH
HOH
428
A
HOH
31
7
HOH
HOH
429
A
HOH
32
7
HOH
HOH
430
A
HOH
33
7
HOH
HOH
431
A
HOH
34
7
HOH
HOH
432
A
HOH
35
7
HOH
HOH
433
A
HOH
36
7
HOH
HOH
434
A
HOH
37
7
HOH
HOH
435
A
HOH
38
7
HOH
HOH
436
A
HOH
39
7
HOH
HOH
437
A
HOH
40
7
HOH
HOH
438
A
HOH
41
7
HOH
HOH
439
A
HOH
44
7
HOH
HOH
440
A
HOH
45
7
HOH
HOH
441
A
HOH
46
7
HOH
HOH
442
A
HOH
47
7
HOH
HOH
443
A
HOH
48
7
HOH
HOH
444
A
HOH
49
7
HOH
HOH
445
A
HOH
51
7
HOH
HOH
446
A
HOH
52
7
HOH
HOH
447
A
HOH
53
7
HOH
HOH
448
A
HOH
54
7
HOH
HOH
449
A
HOH
55
7
HOH
HOH
450
A
HOH
56
7
HOH
HOH
451
A
HOH
57
7
HOH
HOH
452
A
HOH
58
7
HOH
HOH
453
A
HOH
59
7
HOH
HOH
454
A
HOH
60
7
HOH
HOH
455
A
HOH
62
7
HOH
HOH
456
A
HOH
63
7
HOH
HOH
457
A
HOH
65
7
HOH
HOH
458
A
HOH
66
7
HOH
HOH
459
A
HOH
67
7
HOH
HOH
460
A
HOH
68
7
HOH
HOH
461
A
HOH
70
7
HOH
HOH
462
A
HOH
72
7
HOH
HOH
463
A
HOH
73
7
HOH
HOH
464
A
HOH
74
7
HOH
HOH
465
A
HOH
75
7
HOH
HOH
466
A
HOH
76
7
HOH
HOH
467
A
HOH
77
7
HOH
HOH
468
A
HOH
78
7
HOH
HOH
469
A
HOH
79
7
HOH
HOH
470
A
HOH
80
7
HOH
HOH
471
A
HOH
81
7
HOH
HOH
472
A
HOH
83
7
HOH
HOH
473
A
HOH
86
7
HOH
HOH
474
A
HOH
87
7
HOH
HOH
475
A
HOH
88
7
HOH
HOH
476
A
HOH
89
7
HOH
HOH
477
A
HOH
90
7
HOH
HOH
478
A
HOH
91
7
HOH
HOH
479
A
HOH
92
7
HOH
HOH
480
A
HOH
93
7
HOH
HOH
481
A
HOH
94
7
HOH
HOH
482
A
HOH
95
7
HOH
HOH
483
A
HOH
96
7
HOH
HOH
484
A
HOH
97
7
HOH
HOH
485
A
HOH
98
7
HOH
HOH
486
A
HOH
99
7
HOH
HOH
487
A
HOH
100
7
HOH
HOH
488
A
HOH
101
7
HOH
HOH
489
A
HOH
102
7
HOH
HOH
490
A
HOH
103
7
HOH
HOH
491
A
HOH
106
7
HOH
HOH
492
A
HOH
108
7
HOH
HOH
493
A
HOH
109
7
HOH
HOH
494
A
HOH
110
7
HOH
HOH
495
A
HOH
112
7
HOH
HOH
496
A
HOH
113
7
HOH
HOH
497
A
HOH
114
7
HOH
HOH
498
A
HOH
115
7
HOH
HOH
499
A
HOH
116
7
HOH
HOH
500
A
HOH
122
7
HOH
HOH
501
A
HOH
123
7
HOH
HOH
502
A
HOH
124
7
HOH
HOH
503
A
HOH
127
7
HOH
HOH
504
A
HOH
129
7
HOH
HOH
505
A
HOH
130
7
HOH
HOH
506
A
HOH
132
7
HOH
HOH
507
A
HOH
133
7
HOH
HOH
508
A
HOH
135
7
HOH
HOH
509
A
HOH
137
7
HOH
HOH
510
A
HOH
138
7
HOH
HOH
511
A
HOH
140
7
HOH
HOH
512
A
HOH
141
7
HOH
HOH
513
A
HOH
142
7
HOH
HOH
514
A
HOH
143
7
HOH
HOH
515
A
HOH
144
7
HOH
HOH
516
A
HOH
145
7
HOH
HOH
517
A
HOH
146
7
HOH
HOH
518
A
HOH
149
7
HOH
HOH
519
A
HOH
150
7
HOH
HOH
520
A
HOH
151
7
HOH
HOH
521
A
HOH
152
7
HOH
HOH
522
A
HOH
153
7
HOH
HOH
523
A
HOH
154
7
HOH
HOH
524
A
HOH
155
7
HOH
HOH
525
A
HOH
156
7
HOH
HOH
526
A
HOH
157
7
HOH
HOH
527
A
HOH
158
7
HOH
HOH
528
A
HOH
159
7
HOH
HOH
529
A
HOH
160
7
HOH
HOH
530
A
HOH
161
7
HOH
HOH
531
A
HOH
162
7
HOH
HOH
532
A
HOH
168
7
HOH
HOH
533
A
HOH
169
7
HOH
HOH
534
A
HOH
172
7
HOH
HOH
535
A
HOH
173
7
HOH
HOH
536
A
HOH
174
7
HOH
HOH
537
A
HOH
179
7
HOH
HOH
538
A
HOH
183
7
HOH
HOH
539
A
HOH
184
7
HOH
HOH
540
A
HOH
188
7
HOH
HOH
541
A
HOH
189
7
HOH
HOH
542
A
HOH
197
7
HOH
HOH
543
A
HOH
203
7
HOH
HOH
544
A
HOH
205
7
HOH
HOH
545
A
HOH
207
7
HOH
HOH
546
A
HOH
208
7
HOH
HOH
547
A
HOH
209
7
HOH
HOH
548
A
HOH
212
7
HOH
HOH
549
A
HOH
213
7
HOH
HOH
550
A
HOH
214
7
HOH
HOH
551
A
HOH
215
7
HOH
HOH
552
A
HOH
217
7
HOH
HOH
553
A
HOH
218
7
HOH
HOH
554
A
HOH
219
7
HOH
HOH
555
A
HOH
221
7
HOH
HOH
556
A
HOH
222
7
HOH
HOH
557
A
HOH
225
7
HOH
HOH
558
A
HOH
228
7
HOH
HOH
559
A
HOH
229
7
HOH
HOH
560
A
HOH
230
7
HOH
HOH
561
A
HOH
231
7
HOH
HOH
562
A
HOH
233
7
HOH
HOH
563
A
HOH
234
7
HOH
HOH
564
A
HOH
236
7
HOH
HOH
565
A
HOH
238
7
HOH
HOH
566
A
HOH
239
7
HOH
HOH
567
A
HOH
241
7
HOH
HOH
568
A
HOH
243
7
HOH
HOH
569
A
HOH
244
7
HOH
HOH
570
A
HOH
245
7
HOH
HOH
571
A
HOH
246
7
HOH
HOH
572
A
HOH
247
7
HOH
HOH
573
A
HOH
249
7
HOH
HOH
574
A
HOH
251
7
HOH
HOH
575
A
HOH
252
7
HOH
HOH
576
A
HOH
253
7
HOH
HOH
577
A
HOH
254
7
HOH
HOH
578
A
HOH
255
7
HOH
HOH
579
A
HOH
257
7
HOH
HOH
580
A
HOH
259
7
HOH
HOH
581
A
HOH
262
7
HOH
HOH
582
A
HOH
264
7
HOH
HOH
583
A
HOH
265
7
HOH
HOH
584
A
HOH
266
7
HOH
HOH
585
A
HOH
267
7
HOH
HOH
586
A
HOH
268
7
HOH
HOH
587
A
GLY
0
n
1
GLY
0
A
MSE
1
n
2
MSE
1
A
MSE
2
n
3
MSE
2
A
LYS
3
n
4
LYS
3
A
THR
4
n
5
THR
4
A
ILE
5
n
6
ILE
5
A
GLU
6
n
7
GLU
6
A
LEU
7
n
8
LEU
7
A
GLU
8
n
9
GLU
8
A
LYS
9
n
10
LYS
9
A
GLU
10
n
11
GLU
10
A
GLU
11
n
12
GLU
11
A
ILE
12
n
13
ILE
12
A
TYR
13
n
14
TYR
13
A
CYS
14
n
15
CYS
14
A
GLY
15
n
16
GLY
15
A
ASN
16
n
17
ASN
16
A
LEU
17
n
18
LEU
17
A
LEU
18
n
19
LEU
18
A
LEU
19
n
20
LEU
19
A
VAL
20
n
21
VAL
20
A
ASN
21
n
22
ASN
21
A
LYS
22
n
23
LYS
22
A
ASN
23
n
24
ASN
23
A
TYR
24
n
25
TYR
24
A
PRO
25
n
26
PRO
25
A
LEU
26
n
27
LEU
26
A
ARG
27
n
28
ARG
27
A
ASP
28
n
29
ASP
28
A
ASN
29
n
30
ASN
29
A
ASN
30
n
31
ASN
30
A
VAL
31
n
32
VAL
31
A
LYS
32
n
33
LYS
32
A
GLY
33
n
34
GLY
33
A
LEU
34
n
35
LEU
34
A
VAL
35
n
36
VAL
35
A
PRO
36
n
37
PRO
36
A
ALA
37
n
38
ALA
37
A
ASP
38
n
39
ASP
38
A
ILE
39
n
40
ILE
39
A
ARG
40
n
41
ARG
40
A
PHE
41
n
42
PHE
41
A
PRO
42
n
43
PRO
42
A
ASN
43
n
44
ASN
43
A
ILE
44
n
45
ILE
44
A
LEU
45
n
46
LEU
45
A
MSE
46
n
47
MSE
46
A
LYS
47
n
48
LYS
47
A
ARG
48
n
49
ARG
48
A
ASP
49
n
50
ASP
49
A
VAL
50
n
51
VAL
50
A
ALA
51
n
52
ALA
51
A
ASN
52
n
53
ASN
52
A
VAL
53
n
54
VAL
53
A
LEU
54
n
55
LEU
54
A
GLN
55
n
56
GLN
55
A
LEU
56
n
57
LEU
56
A
ILE
57
n
58
ILE
57
A
PHE
58
n
59
PHE
58
A
GLU
59
n
60
GLU
59
A
LYS
60
n
61
LYS
60
A
ILE
61
n
62
ILE
61
A
SER
62
n
63
SER
62
A
ALA
63
n
64
ALA
63
A
GLY
64
n
65
GLY
64
A
ASN
65
n
66
ASN
65
A
SER
66
n
67
SER
66
A
ILE
67
n
68
ILE
67
A
VAL
68
n
69
VAL
68
A
PRO
69
n
70
PRO
69
A
VAL
70
n
71
VAL
70
A
SER
71
n
72
SER
71
A
GLY
72
n
73
GLY
72
A
TYR
73
n
74
TYR
73
A
ARG
74
n
75
ARG
74
A
SER
75
n
76
SER
75
A
LEU
76
n
77
LEU
76
A
GLU
77
n
78
GLU
77
A
GLU
78
n
79
GLU
78
A
GLN
79
n
80
GLN
79
A
THR
80
n
81
THR
80
A
ALA
81
n
82
ALA
81
A
ILE
82
n
83
ILE
82
A
TYR
83
n
84
TYR
83
A
ASP
84
n
85
ASP
84
A
GLY
85
n
86
GLY
85
A
SER
86
n
87
SER
86
A
LEU
87
n
88
LEU
87
A
LYS
88
n
89
LYS
88
A
ASP
89
n
90
ASP
89
A
ASN
90
n
91
ASN
90
A
GLY
91
n
92
GLY
91
A
GLU
92
n
93
GLU
92
A
ASP
93
n
94
ASP
93
A
PHE
94
n
95
PHE
94
A
THR
95
n
96
THR
95
A
ARG
96
n
97
ARG
96
A
LYS
97
n
98
LYS
97
A
TYR
98
n
99
TYR
98
A
VAL
99
n
100
VAL
99
A
ALA
100
n
101
ALA
100
A
LEU
101
n
102
LEU
101
A
PRO
102
n
103
PRO
102
A
ASN
103
n
104
ASN
103
A
HIS
104
n
105
HIS
104
A
SER
105
n
106
SER
105
A
GLU
106
n
107
GLU
106
A
HIS
107
n
108
HIS
107
A
GLN
108
n
109
GLN
108
A
THR
109
n
110
THR
109
A
GLY
110
n
111
GLY
110
A
LEU
111
n
112
LEU
111
A
ALA
112
n
113
ALA
112
A
ILE
113
n
114
ILE
113
A
ASP
114
n
115
ASP
114
A
LEU
115
n
116
LEU
115
A
GLY
116
n
117
GLY
116
A
LEU
117
n
118
LEU
117
A
ASN
118
n
119
ASN
118
A
LYS
119
n
120
LYS
119
A
LYS
120
n
121
LYS
120
A
ASP
121
n
122
ASP
121
A
ILE
122
n
123
ILE
122
A
ASP
123
n
124
ASP
123
A
PHE
124
n
125
PHE
124
A
ILE
125
n
126
ILE
125
A
ARG
126
n
127
ARG
126
A
PRO
127
n
128
PRO
127
A
ASP
128
n
129
ASP
128
A
PHE
129
n
130
PHE
129
A
PRO
130
n
131
PRO
130
A
TYR
131
n
132
TYR
131
A
ASP
132
n
133
ASP
132
A
GLY
133
n
134
GLY
133
A
ILE
134
n
135
ILE
134
A
CYS
135
n
136
CYS
135
A
ASP
136
n
137
ASP
136
A
GLU
137
n
138
GLU
137
A
PHE
138
n
139
PHE
138
A
ARG
139
n
140
ARG
139
A
ARG
140
n
141
ARG
140
A
ALA
141
n
142
ALA
141
A
ALA
142
n
143
ALA
142
A
PRO
143
n
144
PRO
143
A
ASP
144
n
145
ASP
144
A
TYR
145
n
146
TYR
145
A
GLY
146
n
147
GLY
146
A
PHE
147
n
148
PHE
147
A
THR
148
n
149
THR
148
A
GLN
149
n
150
GLN
149
A
ARG
150
n
151
ARG
150
A
TYR
151
n
152
TYR
151
A
ALA
152
n
153
ALA
152
A
ARG
153
n
154
ARG
153
A
ASP
154
n
155
ASP
154
A
LYS
155
n
156
LYS
155
A
GLU
156
n
157
GLU
156
A
GLU
157
n
158
GLU
157
A
ILE
158
n
159
ILE
158
A
THR
159
n
160
THR
159
A
GLY
160
n
161
GLY
160
A
ILE
161
n
162
ILE
161
A
SER
162
n
163
SER
162
A
HIS
163
n
164
HIS
163
A
GLU
164
n
165
GLU
164
A
PRO
165
n
166
PRO
165
A
TRP
166
n
167
TRP
166
A
HIS
167
n
168
HIS
167
A
PHE
168
n
169
PHE
168
A
ARG
169
n
170
ARG
169
A
TYR
170
n
171
TYR
170
A
VAL
171
n
172
VAL
171
A
GLY
172
n
173
GLY
172
A
TYR
173
n
174
TYR
173
A
PRO
174
n
175
PRO
174
A
HIS
175
n
176
HIS
175
A
SER
176
n
177
SER
176
A
LYS
177
n
178
LYS
177
A
ILE
178
n
179
ILE
178
A
MSE
179
n
180
MSE
179
A
GLN
180
n
181
GLN
180
A
GLU
181
n
182
GLU
181
A
ASN
182
n
183
ASN
182
A
GLY
183
n
184
GLY
183
A
PHE
184
n
185
PHE
184
A
SER
185
n
186
SER
185
A
LEU
186
n
187
LEU
186
A
GLU
187
n
188
GLU
187
A
GLU
188
n
189
GLU
188
A
TYR
189
n
190
TYR
189
A
THR
190
n
191
THR
190
A
GLN
191
n
192
GLN
191
A
PHE
192
n
193
PHE
192
A
ILE
193
n
194
ILE
193
A
LYS
194
n
195
LYS
194
A
ALA
195
n
196
ALA
195
A
TYR
196
n
197
TYR
196
A
LEU
197
n
198
LEU
197
A
GLU
198
n
199
GLU
198
A
ASP
199
n
200
ASP
199
A
ASN
200
n
201
ASN
200
A
LYS
201
n
202
LYS
201
A
TYR
202
n
203
TYR
202
A
LEU
203
n
204
LEU
203
A
PHE
204
n
205
PHE
204
A
GLU
205
n
206
GLU
205
A
GLN
206
n
207
GLN
206
A
ALA
207
n
208
ALA
207
A
HIS
208
n
209
HIS
208
A
ARG
209
n
210
ARG
209
A
ALA
210
n
211
ALA
210
A
GLU
211
n
212
GLU
211
A
ILE
212
n
213
ILE
212
A
GLU
213
n
214
GLU
213
A
ILE
214
n
215
ILE
214
A
TYR
215
n
216
TYR
215
A
TYR
216
n
217
TYR
216
A
VAL
217
n
218
VAL
217
A
PRO
218
n
219
PRO
218
A
ALA
219
n
220
ALA
219
A
LYS
220
n
221
LYS
220
A
ASP
221
n
222
ASP
221
A
ASP
222
n
223
ASP
222
A
LYS
223
n
224
LYS
223
A
THR
224
n
225
THR
224
A
LEU
225
n
226
LEU
225
A
ILE
226
n
227
ILE
226
A
LYS
227
n
228
LYS
227
A
ILE
228
n
229
ILE
228
A
PRO
229
n
230
PRO
229
A
GLU
230
n
231
GLU
230
A
ASN
231
n
232
ASN
231
A
CYS
232
n
233
CYS
232
A
VAL
233
n
234
VAL
233
A
TYR
234
n
235
TYR
234
A
GLN
235
n
236
GLN
235
A
ILE
236
n
237
ILE
236
A
SER
237
n
238
SER
237
A
GLY
238
n
239
GLY
238
A
ASN
239
n
240
ASN
239
A
ASN
240
n
241
ASN
240
A
ILE
241
n
242
ILE
241
A
ASP
242
n
243
ASP
242
A
GLY
243
n
244
GLY
243
A
PHE
244
n
245
PHE
244
A
VAL
245
n
246
VAL
245
A
VAL
246
n
247
VAL
246
A
THR
247
n
248
THR
247
A
ILE
248
n
249
ILE
248
A
TRP
249
n
250
TRP
249
A
ARG
250
n
251
ARG
250
A
n
252
251
A
n
253
252
A
n
254
253
A
n
255
254
A
0.3823
0.0117
0.5165
0.7702
-0.0827
1.4629
-0.0166
-0.3294
-0.2666
0.1715
0.0401
0.1086
0.1831
-0.0589
-0.0657
0.1352
-0.0144
0.0118
0.1233
0.0325
0.1346
refined
-13.4764
-13.8820
-18.1936
X-RAY DIFFRACTION
1.0575
-0.4240
-0.5374
1.6291
0.7564
3.0137
0.0413
-0.0201
0.0131
-0.0517
-0.0586
0.0985
0.0093
-0.1347
0.0057
0.0502
-0.0142
-0.0138
0.0542
0.0050
0.1032
refined
-17.2558
-5.3482
-31.1827
X-RAY DIFFRACTION
2.6162
-0.6600
-0.0608
2.2842
-0.2919
2.1523
0.0153
-0.0502
0.1704
-0.0675
0.0561
0.0946
-0.2049
-0.1041
-0.0282
0.0715
-0.0035
0.0197
0.0411
-0.0185
0.0841
refined
-11.8754
3.1163
-23.7725
X-RAY DIFFRACTION
2.7849
0.4257
0.4265
3.8666
-0.5094
3.0980
-0.0539
-0.6402
-0.0715
0.7326
-0.0311
0.0969
0.2433
-0.0655
0.0156
0.1725
0.0405
-0.0385
0.2656
0.0223
0.0305
refined
-3.1852
-8.8349
-5.4101
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
chain A and resi 0:50
X-RAY DIFFRACTION
2
chain A and resi 51:116
X-RAY DIFFRACTION
3
chain A and resi 117:194
X-RAY DIFFRACTION
4
chain A and resi 195:250
author_and_software_defined_assembly
PISA
1
monomeric
A
ASP
114
A
OD1
ASP
115
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HIS
167
A
ND1
HIS
168
1_555
91.9
A
ASP
114
A
OD1
ASP
115
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HOH
418
R
O
HOH
1_555
99.2
A
HIS
167
A
ND1
HIS
168
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HOH
418
R
O
HOH
1_555
94.0
A
ASP
114
A
OD1
ASP
115
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HIS
107
A
NE2
HIS
108
1_555
95.7
A
HIS
167
A
ND1
HIS
168
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HIS
107
A
NE2
HIS
108
1_555
101.5
A
HOH
418
R
O
HOH
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HIS
107
A
NE2
HIS
108
1_555
158.1
A
ASP
114
A
OD1
ASP
115
1_555
A
ZN
301
B
ZN
ZN
1_555
A
ASP
114
A
OD2
ASP
115
1_555
55.2
A
HIS
167
A
ND1
HIS
168
1_555
A
ZN
301
B
ZN
ZN
1_555
A
ASP
114
A
OD2
ASP
115
1_555
147.1
A
HOH
418
R
O
HOH
1_555
A
ZN
301
B
ZN
ZN
1_555
A
ASP
114
A
OD2
ASP
115
1_555
92.2
A
HIS
107
A
NE2
HIS
108
1_555
A
ZN
301
B
ZN
ZN
1_555
A
ASP
114
A
OD2
ASP
115
1_555
83.3
A
ASP
114
A
OD1
ASP
115
1_555
A
ZN
301
B
ZN
ZN
1_555
A
SO4
303
D
O2
SO4
1_555
151.7
A
HIS
167
A
ND1
HIS
168
1_555
A
ZN
301
B
ZN
ZN
1_555
A
SO4
303
D
O2
SO4
1_555
116.4
A
HOH
418
R
O
HOH
1_555
A
ZN
301
B
ZN
ZN
1_555
A
SO4
303
D
O2
SO4
1_555
79.0
A
HIS
107
A
NE2
HIS
108
1_555
A
ZN
301
B
ZN
ZN
1_555
A
SO4
303
D
O2
SO4
1_555
80.2
A
ASP
114
A
OD2
ASP
115
1_555
A
ZN
301
B
ZN
ZN
1_555
A
SO4
303
D
O2
SO4
1_555
96.5
A
MSE
1
SELENOMETHIONINE
A
MSE
2
MET
A
MSE
2
SELENOMETHIONINE
A
MSE
3
MET
A
MSE
46
SELENOMETHIONINE
A
MSE
47
MET
A
MSE
179
SELENOMETHIONINE
A
MSE
180
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
A
N
LYS
3
A
N
LYS
4
A
O
ILE
228
A
O
ILE
229
A
N
VAL
35
A
N
VAL
36
A
O
MSE
46
A
O
MSE
47
A
N
VAL
70
A
N
VAL
71
A
O
ASP
114
A
O
ASP
115
A
N
ILE
113
A
N
ILE
114
A
O
PHE
168
A
O
PHE
169
A
O
ARG
169
A
O
ARG
170
A
N
THR
148
A
N
THR
149
A
N
PHE
204
A
N
PHE
205
A
O
ILE
212
A
O
ILE
213
A
N
GLU
213
A
N
GLU
214
A
O
ILE
248
A
O
ILE
249
A
O
TRP
249
A
O
TRP
250
A
N
VAL
233
A
N
VAL
234
1
A
LYS
251
A
LYS
252
1
Y
1
A
THR
252
A
THR
253
1
Y
1
A
ASP
253
A
ASP
254
1
Y
1
A
ASP
254
A
ASP
255
1
Y
1
A
A
O4
O
SO4
HOH
303
483
2.17
1
A
ASP
121
-93.20
51.54
1
A
TYR
131
-96.39
39.91
1
A
HIS
163
-37.40
122.11
1
A
ASN
200
-155.63
67.33
1
A
ASN
200
-151.60
59.19
1
A
GLN
206
-103.08
-79.85
1
A
ALA
207
-177.20
105.97
1
A
HIS
208
-26.39
117.57
1
A
ARG
209
56.21
-140.97
1
A
ASP
222
-116.75
-96.12
1
A
ASN
231
-78.69
39.66
1
A
ILE
241
-127.26
-58.31
1
A
ASP
242
-155.66
-0.20
-1.7143
0.0000
-4.2779
1.3494
-0.0000
0.3648
0.1864
0.1536
0.1554
1.950
39.584
949
19734
4.99
98.35
0.19
random
1
THROUGHOUT
1.35
SAD
18.50
0.73
1.00
ML
FLAT BULK SOLVENT MODEL
48.654
0.399
1.950
39.584
187
2306
65
0
2054
0.016
2201
1.494
2966
14.268
840
0.116
310
0.007
386
0.2775
0.2171
2.0027
123
2747
98.00
0.2068
0.1947
2.0617
146
2708
98.00
0.2173
0.1755
2.1282
144
2768
98.00
0.2052
0.1596
2.2043
137
2715
98.00
0.2152
0.1600
2.2925
146
2811
98.00
0.1972
0.1557
2.3968
151
2673
98.00
0.2262
0.1580
2.5232
151
2766
98.00
0.1956
0.1529
2.6812
136
2757
99.00
0.1882
0.1515
2.8882
152
2757
99.00
0.1934
0.1497
3.1787
153
2758
99.00
0.1718
0.1439
3.6384
145
2772
99.00
0.1564
0.1227
4.5829
147
2756
99.00
0.1556
0.1596
39.5926
144
2738
98.00
1.95
79.17
4F78
19747
0
-3
0.078
1
10.6
3.3
100.0
0.329
1.95
2.06
3.6
2850
1
3.3
100.0
data collection
HKL-3000
model building
PHENIX
(phenix.autosol)
refinement
PHENIX
(phenix.refine: 1.7.3_928)
data reduction
XDS
data scaling
SCALA
phasing
PHENIX
Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg
Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
5
N
N
5
N
N
5
N
N
5
N
N
5
N
N
5
N
N
5
N
N
6
N
N
6
N
N
6
N
N
7
N
N
A
GLU
10
A
GLU
11
HELX_P
A
CYS
14
A
CYS
15
5
1
5
A
ARG
48
A
ARG
49
HELX_P
A
ILE
61
A
ILE
62
1
2
14
A
SER
75
A
SER
76
HELX_P
A
GLY
91
A
GLY
92
1
3
17
A
GLY
91
A
GLY
92
HELX_P
A
VAL
99
A
VAL
100
1
4
9
A
SER
105
A
SER
106
HELX_P
A
GLY
110
A
GLY
111
5
5
6
A
ASP
132
A
ASP
133
HELX_P
A
ALA
142
A
ALA
143
1
6
11
A
PRO
143
A
PRO
144
HELX_P
A
TYR
145
A
TYR
146
5
7
3
A
ALA
152
A
ALA
153
HELX_P
A
ASP
154
A
ASP
155
5
8
3
A
LYS
155
A
LYS
156
HELX_P
A
GLY
160
A
GLY
161
1
9
6
A
PRO
174
A
PRO
175
HELX_P
A
GLY
183
A
GLY
184
1
10
10
A
SER
185
A
SER
186
HELX_P
A
LYS
194
A
LYS
195
1
11
10
covale
1.335
A
GLY
0
A
C
GLY
1
1_555
A
MSE
1
A
N
MSE
2
1_555
covale
1.331
A
MSE
1
A
C
MSE
2
1_555
A
MSE
2
A
N
MSE
3
1_555
covale
1.328
A
MSE
2
A
C
MSE
3
1_555
A
LYS
3
A
N
LYS
4
1_555
covale
1.328
A
A
LEU
45
A
C
LEU
46
1_555
A
MSE
46
A
N
MSE
47
1_555
covale
1.336
B
A
LEU
45
A
C
LEU
46
1_555
A
MSE
46
A
N
MSE
47
1_555
covale
1.326
A
A
MSE
46
A
C
MSE
47
1_555
A
LYS
47
A
N
LYS
48
1_555
covale
1.333
B
A
MSE
46
A
C
MSE
47
1_555
A
LYS
47
A
N
LYS
48
1_555
covale
1.329
A
ILE
178
A
C
ILE
179
1_555
A
MSE
179
A
N
MSE
180
1_555
covale
1.327
A
MSE
179
A
C
MSE
180
1_555
A
GLN
180
A
N
GLN
181
1_555
metalc
2.180
A
ASP
114
A
OD1
ASP
115
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.192
A
HIS
167
A
ND1
HIS
168
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.205
A
ZN
301
B
ZN
ZN
1_555
A
HOH
418
R
O
HOH
1_555
metalc
2.228
A
HIS
107
A
NE2
HIS
108
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.558
A
ASP
114
A
OD2
ASP
115
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.700
A
ZN
301
B
ZN
ZN
1_555
A
SO4
303
D
O2
SO4
1_555
HYDROLASE
CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, NIAID, ALPHA+BETA PROTEIN, METALLOPEPTIDASE, HEDGEHOG/DD-PEPTIDASE FOLD, MEROPS M15B SUBFAMILY, ZN2+-DEPENDENT D, D-DIPEPTIDASE, VANCOMYCIN RESISTANCE, D-ALANINE-D-ALANINE, HYDROLASE
A
TYR
173
A
TYR
174
1
A
PRO
174
A
PRO
175
4.71
A
HIS
208
A
HIS
209
1
A
ARG
209
A
ARG
210
-10.50
Q9KHL8_ENTFL
UNP
1
1
Q9KHL8
MMKTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNILMKRDVANVLQLIFEKISAGNSIVPVSGYRSLEEQT
AIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGFTQRYARDKEEITG
ISHEPWHFRYVGYPHSKIMQENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDKTLIKIPENCVYQISGNN
IDGFVVTIWRKTDD
1
254
4F78
1
254
Q9KHL8
A
1
2
255
1
EXPRESSION TAG
GLY
0
4F78
A
Q9KHL8
UNP
1
2
2
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
MSE
2
A
MSE
3
A
GLU
8
A
GLU
9
A
LYS
223
A
LYS
224
A
PRO
229
A
PRO
230
A
LEU
34
A
LEU
35
A
PRO
36
A
PRO
37
A
LEU
45
A
LEU
46
A
LYS
47
A
LYS
48
A
ILE
67
A
ILE
68
A
SER
71
A
SER
72
A
ALA
112
A
ALA
113
A
LEU
117
A
LEU
118
A
HIS
167
A
HIS
168
A
TYR
170
A
TYR
171
A
PHE
147
A
PHE
148
A
GLN
149
A
GLN
150
A
TYR
202
A
TYR
203
A
GLU
205
A
GLU
206
A
GLU
211
A
GLU
212
A
PRO
218
A
PRO
219
A
GLY
243
A
GLY
244
A
TRP
249
A
TRP
250
A
VAL
233
A
VAL
234
A
GLY
238
A
GLY
239
BINDING SITE FOR RESIDUE ZN A 301
Software
5
BINDING SITE FOR RESIDUE CL A 302
Software
4
BINDING SITE FOR RESIDUE SO4 A 303
Software
11
BINDING SITE FOR RESIDUE EDO A 304
Software
3
BINDING SITE FOR RESIDUE EDO A 305
Software
7
BINDING SITE FOR RESIDUE EDO A 306
Software
3
BINDING SITE FOR RESIDUE EDO A 307
Software
5
BINDING SITE FOR RESIDUE EDO A 308
Software
2
BINDING SITE FOR RESIDUE EDO A 309
Software
4
BINDING SITE FOR RESIDUE EDO A 310
Software
5
BINDING SITE FOR RESIDUE EDO A 311
Software
4
BINDING SITE FOR RESIDUE EDO A 312
Software
4
BINDING SITE FOR RESIDUE EDO A 313
Software
3
BINDING SITE FOR RESIDUE GOL A 314
Software
3
BINDING SITE FOR RESIDUE GOL A 315
Software
3
BINDING SITE FOR RESIDUE GOL A 316
Software
7
A
HIS
107
A
HIS
108
5
1_555
A
ASP
114
A
ASP
115
5
1_555
A
HIS
167
A
HIS
168
5
1_555
A
SO4
303
D
SO4
5
1_555
A
HOH
418
R
HOH
5
1_555
A
MSE
2
A
MSE
3
4
1_555
A
LYS
3
A
LYS
4
4
1_555
A
THR
4
A
THR
5
4
1_555
A
LYS
227
A
LYS
228
4
1_555
A
ARG
74
A
ARG
75
11
1_555
A
GLN
79
A
GLN
80
11
1_555
A
VAL
99
A
VAL
100
11
1_555
A
ALA
100
A
ALA
101
11
1_555
A
SER
105
A
SER
106
11
1_555
A
HIS
107
A
HIS
108
11
1_555
A
HIS
167
A
HIS
168
11
1_555
A
ZN
301
B
ZN
11
1_555
A
HOH
424
R
HOH
11
1_555
A
HOH
460
R
HOH
11
1_555
A
HOH
483
R
HOH
11
1_555
A
LYS
120
A
LYS
121
3
1_655
A
GLU
157
A
GLU
158
3
1_555
A
EDO
310
K
EDO
3
1_555
A
PRO
36
A
PRO
37
7
1_555
A
ALA
37
A
ALA
38
7
1_555
A
ASN
52
A
ASN
53
7
1_555
A
GLN
191
A
GLN
192
7
1_455
A
HOH
442
R
HOH
7
1_455
A
HOH
512
R
HOH
7
1_455
A
HOH
516
R
HOH
7
1_555
A
GLU
188
A
GLU
189
3
1_555
A
PHE
192
A
PHE
193
3
1_555
A
HOH
470
R
HOH
3
1_655
A
PRO
218
A
PRO
219
5
1_555
A
EDO
308
I
EDO
5
1_555
A
HOH
431
R
HOH
5
1_555
A
HOH
491
R
HOH
5
1_555
A
HOH
524
R
HOH
5
1_555
A
ASP
199
A
ASP
200
2
1_555
A
EDO
307
H
EDO
2
1_555
A
ASN
21
A
ASN
22
4
1_555
A
LYS
22
A
LYS
23
4
1_555
A
ILE
158
A
ILE
159
4
1_555
A
THR
159
A
THR
160
4
1_555
A
LYS
97
A
LYS
98
5
1_555
A
GLY
160
A
GLY
161
5
1_555
A
ILE
161
A
ILE
162
5
1_555
A
SER
162
A
SER
163
5
1_555
A
EDO
304
E
EDO
5
1_555
A
GLY
91
A
GLY
92
4
1_555
A
GLU
92
A
GLU
93
4
1_555
A
ASP
93
A
ASP
94
4
1_555
A
HOH
420
R
HOH
4
1_555
A
GLU
181
A
GLU
182
4
1_555
A
PHE
204
A
PHE
205
4
1_555
A
GLU
205
A
GLU
206
4
1_555
A
HOH
584
R
HOH
4
1_555
A
ASP
144
A
ASP
145
3
1_555
A
ARG
209
A
ARG
210
3
1_555
A
HOH
531
R
HOH
3
1_555
A
ALA
152
A
ALA
153
3
1_555
A
ARG
153
A
ARG
154
3
1_555
A
ASP
154
A
ASP
155
3
1_555
A
ASN
65
A
ASN
66
3
1_555
A
SER
66
A
SER
67
3
1_555
A
LYS
155
A
LYS
156
3
1_455
A
CYS
14
A
CYS
15
7
1_555
A
GLY
15
A
GLY
16
7
1_555
A
LEU
18
A
LEU
19
7
1_555
A
VAL
31
A
VAL
32
7
1_555
A
THR
109
A
THR
110
7
1_555
A
HOH
578
R
HOH
7
1_555
A
HOH
585
R
HOH
7
1_555
4
P 1 21 1