1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Simpson, P.J.
Bolam, D.N.
Cooper, A.
Ciruela, A.
Hazlewood, G.P.
Gilbert, H.J.
Williamson, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
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
Structure Fold.Des.
FODEFH
1263
0969-2126
7
853
864
10.1016/S0969-2126(99)80108-7
10425686
A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.
1999
10.2210/pdb2xbd/pdb
pdb_00002xbd
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
8787.418
XYLANASE D
3.2.1.8
XYLAN BINDING DOMAIN 1
1
man
polymer
XBD1, ENDO-1,4-BETA-XYLANASE D
no
no
TGCSVTATRAEEWSDRFNVTYSVSGSSAWTVNLALNGSQTIQASWNANVTGSGSTRTVTPNGSGNTFGVTVMKNGSSTTP
AATCAGS
TGCSVTATRAEEWSDRFNVTYSVSGSSAWTVNLALNGSQTIQASWNANVTGSGSTRTVTPNGSGNTFGVTVMKNGSSTTP
AATCAGS
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
Cellulomonas
Escherichia
sample
1708
Cellulomonas fimi
562
Escherichia coli
JM83
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1999-07-21
1
1
2008-03-25
1
2
2011-07-13
1
3
2022-03-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
Y
BNL
1998-10-27
REL
REL
THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR NMR SPECTROSCOPY ON A UNIFORMLY 15N-LABELLED SAMPLE OF XBD1
MINIMIZED AVERAGE STRUCTURE, CALCULATED FROM 38 LOWEST ENERGY STRUCTURES
50
1
TOCSY
DQF-COSY
NOESY
E.COSY
HSQC
NOESY-HMQC
TOCSY-HMQC
HNHA
HNHB
5.0
310
K
YASAP
HYBRID DISTANCE GEOMETRY/ SIMULATED ANNEALING
BRUNGER
refinement
X-PLOR
3.1
structure solution
MSI FELIX
97.0
500
Bruker
DRX500
600
Bruker
DRX600
800
Bruker
DRX800
THR
247
n
1
THR
247
A
GLY
248
n
2
GLY
248
A
CYS
249
n
3
CYS
249
A
SER
250
n
4
SER
250
A
VAL
251
n
5
VAL
251
A
THR
252
n
6
THR
252
A
ALA
253
n
7
ALA
253
A
THR
254
n
8
THR
254
A
ARG
255
n
9
ARG
255
A
ALA
256
n
10
ALA
256
A
GLU
257
n
11
GLU
257
A
GLU
258
n
12
GLU
258
A
TRP
259
n
13
TRP
259
A
SER
260
n
14
SER
260
A
ASP
261
n
15
ASP
261
A
ARG
262
n
16
ARG
262
A
PHE
263
n
17
PHE
263
A
ASN
264
n
18
ASN
264
A
VAL
265
n
19
VAL
265
A
THR
266
n
20
THR
266
A
TYR
267
n
21
TYR
267
A
SER
268
n
22
SER
268
A
VAL
269
n
23
VAL
269
A
SER
270
n
24
SER
270
A
GLY
271
n
25
GLY
271
A
SER
272
n
26
SER
272
A
SER
273
n
27
SER
273
A
ALA
274
n
28
ALA
274
A
TRP
275
n
29
TRP
275
A
THR
276
n
30
THR
276
A
VAL
277
n
31
VAL
277
A
ASN
278
n
32
ASN
278
A
LEU
279
n
33
LEU
279
A
ALA
280
n
34
ALA
280
A
LEU
281
n
35
LEU
281
A
ASN
282
n
36
ASN
282
A
GLY
283
n
37
GLY
283
A
SER
284
n
38
SER
284
A
GLN
285
n
39
GLN
285
A
THR
286
n
40
THR
286
A
ILE
287
n
41
ILE
287
A
GLN
288
n
42
GLN
288
A
ALA
289
n
43
ALA
289
A
SER
290
n
44
SER
290
A
TRP
291
n
45
TRP
291
A
ASN
292
n
46
ASN
292
A
ALA
293
n
47
ALA
293
A
ASN
294
n
48
ASN
294
A
VAL
295
n
49
VAL
295
A
THR
296
n
50
THR
296
A
GLY
297
n
51
GLY
297
A
SER
298
n
52
SER
298
A
GLY
299
n
53
GLY
299
A
SER
300
n
54
SER
300
A
THR
301
n
55
THR
301
A
ARG
302
n
56
ARG
302
A
THR
303
n
57
THR
303
A
VAL
304
n
58
VAL
304
A
THR
305
n
59
THR
305
A
PRO
306
n
60
PRO
306
A
ASN
307
n
61
ASN
307
A
GLY
308
n
62
GLY
308
A
SER
309
n
63
SER
309
A
GLY
310
n
64
GLY
310
A
ASN
311
n
65
ASN
311
A
THR
312
n
66
THR
312
A
PHE
313
n
67
PHE
313
A
GLY
314
n
68
GLY
314
A
VAL
315
n
69
VAL
315
A
THR
316
n
70
THR
316
A
VAL
317
n
71
VAL
317
A
MET
318
n
72
MET
318
A
LYS
319
n
73
LYS
319
A
ASN
320
n
74
ASN
320
A
GLY
321
n
75
GLY
321
A
SER
322
n
76
SER
322
A
SER
323
n
77
SER
323
A
THR
324
n
78
THR
324
A
THR
325
n
79
THR
325
A
PRO
326
n
80
PRO
326
A
ALA
327
n
81
ALA
327
A
ALA
328
n
82
ALA
328
A
THR
329
n
83
THR
329
A
CYS
330
n
84
CYS
330
A
ALA
331
n
85
ALA
331
A
GLY
332
n
86
GLY
332
A
SER
333
n
87
SER
333
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
THR
252
A
O
THR
6
A
N
SER
268
A
N
SER
22
A
O
PHE
263
A
O
PHE
17
A
N
VAL
317
A
N
VAL
71
A
O
GLY
314
A
O
GLY
68
A
N
TRP
291
A
N
TRP
45
A
O
THR
329
A
O
THR
83
A
N
ASN
278
A
N
ASN
32
A
O
VAL
277
A
O
VAL
31
A
N
VAL
304
A
N
VAL
58
A
O
THR
303
A
O
THR
57
A
N
THR
296
A
N
THR
50
1
A
ARG
255
0.234
SIDE CHAIN
1
A
ARG
262
0.317
SIDE CHAIN
1
A
ARG
302
0.310
SIDE CHAIN
1
A
ALA
256
-92.05
-80.56
1
A
ARG
262
174.80
170.15
1
A
ALA
293
177.79
149.94
1
A
LYS
319
-60.30
-73.88
1
A
THR
325
-47.03
159.68
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
INTERNAL XYLAN BINDING DOMAIN FROM CELLULOMONAS FIMI XYLANASE D, NMR, MINIMIZED AVERAGE STRUCTURE
1
Y
N
disulf
2.020
A
CYS
249
A
SG
CYS
3
1_555
A
CYS
330
A
SG
CYS
84
1_555
HYDROLASE
HYDROLASE, XYLAN BINDING DOMAIN, XYLANASE, BETA-SHEET
XYND_CELFI
UNP
1
1
P54865
MSDSFEATRTTRRRRPLQALTGLLAAGALVAGALAAASPAAAAVTSNTTGTHDGYFYSFWTDSPGSVSMDLNSGGGYTRW
SNTGNFVAGKGWSTGGRKTVSYSGQFNPSRNAYLTLYGWTQSPLVEYYIVDSWGTYRPTGTFMGTVTSDGGTYDIYRTQR
VNKPSIEGDSSTFYQYWSVRQQKRTGGTITSGNHFDAWASKGMNLGRHNYMIMATEGYQSSGSSSITVSEGSGGGGGGDT
GGGGGSTGCSVTATRAEEWSDRFNVTYSVSGSSAWTVNLALNGSQTIQASWNANVTGSGSTRTVTPNGSGNTFGVTVMKN
GSSTTPAATCAGSGGGTATPTPTPTPTPTPQSCSAGYVGLTFDDGPNTGTTNQILSTLTQYGATATVFPTGQNAQGNPSL
MQAYKNAGVQIGNHSWDHPHLVNMSQSDMQSQLTRTQQAIQQTAGVTPTLFRPPYGESNATLRQVESSLGLREIIWDVDS
QDWNNASASQIRQAASRLTNGQIILMHDWPAATVQALPGILQDLRSRNLCTGHISSSTGRAVAPSSAGGGGGGGGGTGSC
SVSAVRGEEWADRFNVTYSVSGSSSWVVTLGLNGGQSVQSSWNAALTGSSGTVTARPNGSGNSFGVTFYKNGSSATPGAT
CATG
247
333
2XBD
247
333
P54865
A
1
1
87
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
252
A
THR
6
A
ARG
255
A
ARG
9
A
ARG
262
A
ARG
16
A
SER
268
A
SER
22
A
THR
312
A
THR
66
A
MET
318
A
MET
72
A
ILE
287
A
ILE
41
A
TRP
291
A
TRP
45
A
ALA
328
A
ALA
82
A
CYS
330
A
CYS
84
A
VAL
277
A
VAL
31
A
LEU
279
A
LEU
33
A
ARG
302
A
ARG
56
A
THR
305
A
THR
59
A
ASN
294
A
ASN
48
A
THR
296
A
THR
50
BINDING SITE TRYPTOPHANS
Unknown
2
A
TRP
259
A
TRP
13
2
1_555
A
TRP
291
A
TRP
45
2
1_555
1
P 1