1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Clore, G.M.
Huth, J.R.
Bewley, C.
Gronenborn, A.M.
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
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
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
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
4
657
665
10.1038/nsb0897-657
9253416
The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.
1997
10.2210/pdb2ezd/pdb
pdb_00002ezd
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3662.404
DNA (5'-D(*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3')
1
syn
polymer
3662.404
DNA (5'-D(*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3')
1
syn
polymer
2727.262
HIGH MOBILITY GROUP PROTEIN HMG-I/HMG-Y
1
man
polymer
HIGH MOBILITY GROUP PROTEIN HMG
no
no
(DG)(DG)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC)(DT)(DC)
GGGAAATTCCTC
B
polydeoxyribonucleotide
no
no
(DG)(DA)(DG)(DG)(DA)(DA)(DT)(DT)(DT)(DC)(DC)(DC)
GAGGAATTTCCC
C
polydeoxyribonucleotide
no
no
VPTPKRPRGRPKGSKNKGAAKTRKT
VPTPKRPRGRPKGSKNKGAAKTRKT
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
human
Homo
Escherichia
sample
9606
Homo sapiens
562
Escherichia coli
3.027
1
19
B
201
C
224
-0.226
B_DG201:DC224_C
1
0.584
-0.504
0.033
-0.190
9.241
1
19
B
202
C
223
-0.935
B_DG202:DC223_C
2
-2.749
-0.190
0.300
-0.022
5.404
1
19
B
203
C
222
-2.266
B_DG203:DC222_C
3
-11.612
0.059
0.371
-0.213
0.034
1
20
B
204
C
221
-4.179
B_DA204:DT221_C
4
-12.391
-0.062
0.515
-0.170
-4.133
1
20
B
205
C
220
-4.307
B_DA205:DT220_C
5
-13.523
0.211
-0.114
-0.203
12.433
1
20
B
206
C
219
-10.661
B_DA206:DT219_C
6
-5.575
-0.187
0.155
-0.056
4.139
1
20
B
207
C
218
-4.326
B_DT207:DA218_C
7
-14.804
-0.027
-0.252
-0.183
-0.429
1
20
B
208
C
217
0.910
B_DT208:DA217_C
8
-16.294
0.240
-0.171
-0.188
-9.655
1
19
B
209
C
216
-0.470
B_DC209:DG216_C
9
-11.591
0.183
0.050
-0.125
-9.334
1
19
B
210
C
215
-2.396
B_DC210:DG215_C
10
-9.423
0.038
-0.274
-0.259
-5.370
1
20
B
211
C
214
-8.928
B_DT211:DA214_C
11
-3.202
0.113
0.116
-0.063
-3.011
1
19
B
212
C
213
1.927
B_DC212:DG213_C
12
0.567
0.485
0.026
-0.171
3.919
36.356
B
B
201
202
-6.288
C
C
224
223
3.955
-3.915
-0.514
0.304
BB_DG201DG202:DC223DC224_CC
1
-1.483
2.381
36.122
1.146
0.574
4.049
35.632
B
B
202
203
0.453
C
C
223
222
4.047
0.277
-0.142
0.137
BB_DG202DG203:DC222DC223_CC
2
-0.226
0.369
35.630
0.175
0.192
3.935
35.409
B
B
203
204
5.612
C
C
222
221
3.943
3.408
-0.149
0.066
BB_DG203DA204:DT221DC222_CC
3
-1.236
2.035
35.229
-0.496
0.026
3.927
35.955
B
B
204
205
1.872
C
C
221
220
3.938
1.155
-0.203
-0.046
BB_DA204DA205:DT220DT221_CC
4
1.055
-1.709
35.922
-0.272
0.510
2.925
33.243
B
B
205
206
-7.080
C
C
220
219
2.921
-4.039
-0.324
-0.086
BB_DA205DA206:DT219DT220_CC
5
-1.946
3.411
32.948
0.457
0.275
4.050
34.626
B
B
206
207
1.642
C
C
219
218
4.049
0.976
0.328
-0.405
BB_DA206DT207:DA218DT219_CC
6
3.010
-5.063
34.485
-0.867
0.024
3.997
38.242
B
B
207
208
-7.587
C
C
218
217
4.046
-4.957
0.459
0.167
BB_DT207DT208:DA217DA218_CC
7
0.390
-0.597
37.929
1.025
-0.641
4.153
39.152
B
B
208
209
-3.607
C
C
217
216
4.188
-2.415
-0.134
0.505
BB_DT208DC209:DG216DA217_CC
8
-1.385
2.068
39.057
1.123
-0.012
3.744
37.646
B
B
209
210
-9.064
C
C
216
215
3.819
-5.827
-0.091
0.198
BB_DC209DC210:DG215DG216_CC
9
0.749
-1.166
37.201
1.186
0.254
3.692
36.311
B
B
210
211
-10.722
C
C
215
214
3.742
-6.645
-0.423
0.028
BB_DC210DT211:DA214DG215_CC
10
-1.491
2.406
35.688
1.110
0.440
4.008
32.911
B
B
211
212
-1.429
C
C
214
213
4.015
-0.809
0.857
0.341
BB_DT211DC212:DG213DA214_CC
11
0.092
-0.162
32.901
0.772
-1.493
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
1997-10-15
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-03-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
ENSEMBLE OF 35 STRUCTURES
Y
BNL
1997-06-04
REL
DATA WERE RECORDED ON A 2:1 COMPLEX OF DNA DODECAMER TO
HMG-I(Y) 50-91 WHICH CONTAINS THE SECOND AND THIRD DNA
DNA BINDING DOMAINS. EACH DNA BINDING DOMAIN BINDS TO
1 MOLECULE OF DNA.
35
1
6.1
306
K
THE STRUCTURES WERE CALCULATED USING THE SIMULATED
ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT.
229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER)
MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL.
(1984) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON
CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON.
SERIES B 106, 92 - 96) RESTRAINTS AND A CONFORMATIONAL
DATABASE
POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 -
1080
AND (1997) J. MAGN. RESON. 125, 171-177)
THE 3D STRUCTURE OF THE COMPLEX OF THE SECOND DNA BINDING
DOMAIN OF HMG-I(Y)
COMPLEXED TO DNA WAS SOLVED BY
MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR
(A) PROTEIN: 71 SEQUENTIAL (|I-J|=1), 4 MEDIUM
RANGE (1 < |I-J| >=5) AND 64 INTRARESIDUE
APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL
36 TORSION ANGLE RESTRAINTS
13 THREE-BOND HN-HA AND 8 THREE_BOND COCO COUPLING
CONSTANT RESTRAINTS; 39 (21 CALPHA AND 18 CBETA) 13C
SHIFT RESTRAINTS.
(B) DNA: 249 INTRARESIDUE, 119 SEQUENTIAL INTRASTRAND AND
33 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 42
DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 136
TORSION ANGLE RESTRAINTS
(C) 73 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS
(D) 5 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES
(E) 20 'REPULSIVE' RESTRAINTS
THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED
MEAN STRUCTURE. THE LAST NUMERIC COLUMN REPRESENTS THE
RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
FOUND IN PDB ENTRY 2EZE ABOUT THE MEAN COORDINATE
POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA
STRUCTURES HAS NO MEANING.
RESIDUES 3 - 27 OF THE PROTEIN CORRESPOND TO RESIDUES 51 -
75 OF INTACT HMG-I(Y). RESIDUES 3 - 5 AND 20 - 27 ARE
DISORDERED. ONLY RESIDUES 3 - 23 ARE PROVIDED FOR THE
RESTRAINED REGULARIZED MEAN STRUCTURE.
simulated annealing
BRUNGER
refinement
X-PLOR
3.1
structure solution
XPLOR MODIFIED
MODIFIED
600
Bruker
AMX500
500
Bruker
AMX600
750
Bruker
DMX600
750
Bruker
DMX750
G
201
n
1
DG
201
B
G
202
n
2
DG
202
B
G
203
n
3
DG
203
B
A
204
n
4
DA
204
B
A
205
n
5
DA
205
B
A
206
n
6
DA
206
B
T
207
n
7
DT
207
B
T
208
n
8
DT
208
B
C
209
n
9
DC
209
B
C
210
n
10
DC
210
B
T
211
n
11
DT
211
B
C
212
n
12
DC
212
B
G
213
n
1
DG
213
C
A
214
n
2
DA
214
C
G
215
n
3
DG
215
C
G
216
n
4
DG
216
C
A
217
n
5
DA
217
C
A
218
n
6
DA
218
C
T
219
n
7
DT
219
C
T
220
n
8
DT
220
C
T
221
n
9
DT
221
C
C
222
n
10
DC
222
C
C
223
n
11
DC
223
C
C
224
n
12
DC
224
C
VAL
3
n
1
VAL
3
A
PRO
4
n
2
PRO
4
A
THR
5
n
3
THR
5
A
PRO
6
n
4
PRO
6
A
LYS
7
n
5
LYS
7
A
ARG
8
n
6
ARG
8
A
PRO
9
n
7
PRO
9
A
ARG
10
n
8
ARG
10
A
GLY
11
n
9
GLY
11
A
ARG
12
n
10
ARG
12
A
PRO
13
n
11
PRO
13
A
LYS
14
n
12
LYS
14
A
GLY
15
n
13
GLY
15
A
SER
16
n
14
SER
16
A
LYS
17
n
15
LYS
17
A
ASN
18
n
16
ASN
18
A
LYS
19
n
17
LYS
19
A
GLY
20
n
18
GLY
20
A
ALA
21
n
19
ALA
21
A
ALA
22
n
20
ALA
22
A
LYS
23
n
21
LYS
23
A
n
22
24
A
n
23
25
A
n
24
26
A
n
25
27
A
author_defined_assembly
3
trimeric
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
1
A
THR
24
C
THR
22
1
Y
1
A
ARG
25
C
ARG
23
1
Y
1
A
LYS
26
C
LYS
24
1
Y
1
A
THR
27
C
THR
25
1
Y
1
A
PRO
6
-49.94
81.01
1
A
PRO
13
-42.71
153.61
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
SOLUTION STRUCTURE OF A COMPLEX OF THE SECOND DNA BINDING DOMAIN OF HUMAN HMG-I(Y) BOUND TO DNA DODECAMER CONTAINING THE PRDII SITE OF THE INTERFERON-BETA PROMOTER, NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
3
N
N
hydrog
WATSON-CRICK
B
DG
201
A
N1
DG
1
1_555
C
DC
224
B
N3
DC
12
1_555
hydrog
WATSON-CRICK
B
DG
201
A
N2
DG
1
1_555
C
DC
224
B
O2
DC
12
1_555
hydrog
WATSON-CRICK
B
DG
201
A
O6
DG
1
1_555
C
DC
224
B
N4
DC
12
1_555
hydrog
WATSON-CRICK
B
DG
202
A
N1
DG
2
1_555
C
DC
223
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
B
DG
202
A
N2
DG
2
1_555
C
DC
223
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
B
DG
202
A
O6
DG
2
1_555
C
DC
223
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
B
DG
203
A
N1
DG
3
1_555
C
DC
222
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
B
DG
203
A
N2
DG
3
1_555
C
DC
222
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
B
DG
203
A
O6
DG
3
1_555
C
DC
222
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
B
DA
204
A
N1
DA
4
1_555
C
DT
221
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
B
DA
204
A
N6
DA
4
1_555
C
DT
221
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
B
DA
205
A
N1
DA
5
1_555
C
DT
220
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
B
DA
205
A
N6
DA
5
1_555
C
DT
220
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
B
DA
206
A
N1
DA
6
1_555
C
DT
219
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
B
DA
206
A
N6
DA
6
1_555
C
DT
219
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
B
DT
207
A
N3
DT
7
1_555
C
DA
218
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
B
DT
207
A
O4
DT
7
1_555
C
DA
218
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
B
DT
208
A
N3
DT
8
1_555
C
DA
217
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
B
DT
208
A
O4
DT
8
1_555
C
DA
217
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
B
DC
209
A
N3
DC
9
1_555
C
DG
216
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
B
DC
209
A
N4
DC
9
1_555
C
DG
216
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
B
DC
209
A
O2
DC
9
1_555
C
DG
216
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
B
DC
210
A
N3
DC
10
1_555
C
DG
215
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
B
DC
210
A
N4
DC
10
1_555
C
DG
215
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
B
DC
210
A
O2
DC
10
1_555
C
DG
215
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
B
DT
211
A
N3
DT
11
1_555
C
DA
214
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
B
DT
211
A
O4
DT
11
1_555
C
DA
214
B
N6
DA
2
1_555
hydrog
WATSON-CRICK
B
DC
212
A
N3
DC
12
1_555
C
DG
213
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
B
DC
212
A
N4
DC
12
1_555
C
DG
213
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
B
DC
212
A
O2
DC
12
1_555
C
DG
213
B
N2
DG
1
1_555
DNA BINDING PROTEIN/DNA
DNA BINDING PROTEIN, MINOR GROOVE DNA BINDING, TRANSCRIPTIONAL CO-ACTIVATOR, ARCHITECTURAL FACTOR, COMPLEX (DNA-BINDING PROTEIN-DNA), DNA BINDING PROTEIN-DNA COMPLEX
HMGIY_HUMAN
UNP
3
P17096
2EZD
PDB
1
2EZD
2EZD
PDB
2
2EZD
39
59
2EZD
3
23
P17096
A
1
1
21
201
212
2EZD
201
212
2EZD
B
2
1
12
213
224
2EZD
213
224
2EZD
C
3
1
12
1
P 1