1ML3

Evidences for a flip-flop catalytic mechanism of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase, from its crystal structure in complex with reacted irreversible inhibitor 2-(2-phosphono-ethyl)-acrylic acid 4-nitro-phenyl ester


Sequence Similarity Clusters for the Entities in PDB 1ML3

Entity #1 | Chains: A,B,C,D
Glyceraldehyde 3-phosphate dehydrogenase, glycosomal protein, length: 359 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name Structural variation in cluster
100 % 5 6 3227
95 % 5 6 3342 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.6
PDBFlex
90 % 5 7 2575
70 % 5 12 1236
50 % 99 151 74
40 % 99 151 97
30 % 99 151 109

Instructions

In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff.



View more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB PDB.

You can also use the structure comparison tool to compare any 2 given structures


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Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 5Y37 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
2 4O59 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 9913 1.2.1.12 | Details
3 4LSM 1 A, B Glyceraldehyde 3-phosphate dehydrogenase, cytosolic 5693 1.2.1.12 | Details
4 2G82 1 A, B, C, D, O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 271 1.2.1.12 | Details
5 5C7O 1 O, P Glyceraldehyde-3-phosphate dehydrogenase, testis-specific unp residues 74-407 9606 1.2.1.12 | Details
6 3H9E 1 O, P Glyceraldehyde-3-phosphate dehydrogenase, testis-specific Residues 69-407 9606 1.2.1.12 | Details
7 1OBF 1 O, P GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 85698 1.2.1.12 | Details
8 3CMC 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1422 1.2.1.12 | Details
9 3LVF 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
10 5TSO 1 P, R, S Glyceraldehyde-3-phosphate dehydrogenase 9823 1.2.1.12 | Details
11 1U8F 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase, liver 9606 1.2.1.12 | Details
12 6IQM 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase, type I 1590 1.2.1.12 | Details
13 1GD1 1 O, P, Q, R HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 1422 1.2.1.12 | Details
14 5UTM 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
15 4WNC 1 A, B, C, D, E, F, G, O Glyceraldehyde-3-phosphate dehydrogenase 9606 1.2.1.12 | Details
16 5UR0 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 5762 1.2.1.12 | Details
17 1DSS 1 G, R D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE NAD+ NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN 150436 1.2.1.12 | Details
18 1GAD 1 O, P D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE WILD TYPE, HOLO FORM 562 1.2.1.12 | Details
19 3IDS 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase, glycosomal 5693 1.2.1.12 | Details
20 5C7L 1 O, R Glyceraldehyde-3-phosphate dehydrogenase, testis-specific unp residues 74-407 9606 1.2.1.12 | Details
21 3PYM 1 A, B Glyceraldehyde-3-phosphate dehydrogenase 3 4932 1.2.1.12 | Details
22 1CRW 1 G, R D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE 150436 1.2.1.12 | Details
23 1SZJ 1 G, R D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE COMPLEX WITH NAD+ NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN 150436 1.2.1.12 | Details
24 4O63 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase UNP residues 2-333 9913 1.2.1.12 | Details
25 5UTL 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
26 3CIF 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 5807 1.2.1.12 | Details
27 5V8Y 1 A, B Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
28 5C7I 1 O, R Glyceraldehyde-3-phosphate dehydrogenase, testis-specific 10090 1.2.1.12 | Details
29 5ZA0 1 A Glyceraldehyde-3-phosphate dehydrogenase A 562 1.2.1.12 | Details
30 1K3T 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 5693 1.2.1.12 | Details
31 5JY6 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
32 5M6D 1 A, B Glyceraldehyde-3-phosphate dehydrogenase The active site cystein is oxidized, this why there seems to be a mismatch between sequence and coordinates, but this is not the case 1313 1.2.1 | Details
33 1NQO 1 A, C, O, Q Glyceraldehyde 3-phosphate dehydrogenase 1422 1.2.1.12 | Details
34 4P8R 1 A, B, C, D Glyceraldehyde 3-phosphate dehydrogenase, cytosolic TrbrA.00855.a.B1 185431 1.2.1.12 | Details
35 3LC1 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
36 3HJA 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 139 1.2.1.12 | Details
37 4BOY 1 A, B GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 146786
38 1RM4 1 A, B, O Glyceraldehyde 3-phosphate dehydrogenase A 3562 1.2.1.13 | Details
39 3PFW 1 O, P Glyceraldehyde-3-phosphate dehydrogenase, testis-specific UNP RESIDUES 69-407 9606 1.2.1.12 | Details
40 1VSV 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 5807 1.2.1.12 | Details
41 2VYN 1 A, B, C GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 562 1.2.1.12 | Details
42 2VYN 2 D GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE POLY PROLINE N-TERMINUS REPLACED RESIDUES 102-432 10116 1.2.1.12 | Details
43 3ZCX 1 A, B GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 146786
44 1S7C 1 A Glyceraldehyde 3-phosphate dehydrogenase A 562 1.2.1.12 | Details
45 1DC5 1 A, B GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE APO 562 1.2.1.12 | Details
46 4K9D 1 A, B, C, D, E, F, G, H Glyceraldehyde-3-phosphate dehydrogenase 6279 1.2.1.12 | Details
47 3CPS 1 A, B Glyceraldehyde 3-phosphate dehydrogenase 5807
48 1NPT 1 O, P, Q, R Glyceraldehyde 3-phosphate dehydrogenase 1422 1.2.1.12 | Details
49 5LD5 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 82135 1.2.1 | Details
50 1DC6 1 A, B GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE HOLO 562 1.2.1.12 | Details
51 1NQA 1 O, P, Q, R Glyceraldehyde 3-phosphate dehydrogenase 1422 1.2.1.12 | Details
52 3QV1 1 A, B, C, D, E, F Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic UNP residues 60-396 3702 1.2.1.13 | Details
53 1NQ5 1 A, C, O, Q Glyceraldehyde 3-phosphate dehydrogenase 1422 1.2.1.12 | Details
54 3V1Y 1 A, B, C, O Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 4530 1.2.1.12 | Details
55 3STH 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 5811 1.2.1.12 | Details
56 3HQ4 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
57 4WNI 1 A, B, C, O Glyceraldehyde-3-phosphate dehydrogenase 9606 1.2.1.12 | Details
58 6IQV 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase, type I 1590 1.2.1.12 | Details
59 5O0V 1 A Glyceraldehyde-3-phosphate dehydrogenase A 562 1.2.1.12 | Details
60 1DBV 1 O, P, Q, R GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE COMPLEXED WITH NAD+ 1422 1.2.1.12 | Details
61 2DBV 1 O, P, Q, R GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE COMPLEXED WITH NADP+ 1422 1.2.1.12 | Details
62 2B4R 1 O, P, Q, R glyceraldehyde-3-phosphate dehydrogenase 5833 1.2.1.12 | Details
63 2X5K 1 O, P, Q, R D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE 562 1.2.1.72 | Details
64 3L4S 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
65 1GAE 1 O, P D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE HOLO FORM 562 1.2.1.12 | Details
66 4DBV 1 O, P, Q, R GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 1422 1.2.1.12 | Details
67 1RM5 1 A, B, O Glyceraldehyde 3-phosphate dehydrogenase A 3562 1.2.1.13 | Details
68 3ZDF 1 A, B GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 146786
69 1VSU 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 5807 1.2.1.12 | Details
70 2EP7 1 A, B Glyceraldehyde-3-phosphate dehydrogenase 63363 1.2.1.12 | Details
71 5J9G 1 A, B Glyceraldehyde-3-p dehydrogenase 1579 1.2.1.12 | Details
72 3KSD 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
73 3DMT 1 A, B, D Glyceraldehyde-3-phosphate dehydrogenase, glycosomal 5693 1.2.1.12 | Details
74 3DMT 2 C Glyceraldehyde-3-phosphate dehydrogenase, glycosomal 5693 1.2.1.12 | Details
75 1RM3 1 A, B, O Glyceraldehyde 3-phosphate dehydrogenase A 3562 1.2.1.13 | Details
76 5JYE 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
77 3L6O 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
78 2VYV 1 A, B, C GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 562 1.2.1.12 | Details
79 2VYV 2 D GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE POLY PROLINE N-TERMINUS REPLACED RESIDUES 102-432 10116 1.2.1.12 | Details
80 3E5R 1 A, B, C, O Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 4530 1.2.1.12 | Details
81 1HDG 1 O, Q HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2336 1.2.1.12 | Details
82 5VMT 1 A, B, C, D, E, F, G, H Glyceraldehyde-3-phosphate dehydrogenase residues 24-357 485 1.2.1 | Details
83 3DOC 1 A, B, C, D glyceraldehyde 3-phosphate dehydrogenase 235
84 2X5J 1 O, P, Q, R D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE COMPLEX WITH PHOSPHATE ANION 562 1.2.1.72 | Details
85 2B4T 1 O, P, Q, R glyceraldehyde-3-phosphate dehydrogenase 5833 1.2.1.12 | Details
86 2GD1 1 O, P, Q, R APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 1422 1.2.1.12 | Details
87 3B1J 1 A, B Glyceraldehyde 3-phosphate dehydrogenase (NADP+) 32046
88 3K73 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
89 2I5P 1 O, P Glyceraldehyde-3-phosphate dehydrogenase 1 4911 1.2.1.12 | Details
90 3K9Q 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
91 1J0X 1 O, P, Q, R glyceraldehyde-3-phosphate dehydrogenase 9986 1.2.1.12 | Details
92 3DBV 1 O, P, Q, R GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 1422 1.2.1.12 | Details
93 3LC7 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
94 1DC3 1 A, B GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE APO 562 1.2.1.12 | Details
95 3KV3 1 O, P, Q, R GAPDH 1280 1.2.1.12 | Details
96 3GNQ 1 A, B, C, D, E, F, G, H Glyceraldehyde-3-phosphate dehydrogenase, type I 28450 1.2.1 | Details
97 6DFZ 1 A, B, C, D, E, F, G, H glyceraldehyde-3-phosphate dehydrogenase 45264 1.2.1.12 | Details
98 1DC4 1 A, B GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 562 1.2.1.12 | Details
99 1ML3 1 A, B, C, D Glyceraldehyde 3-phosphate dehydrogenase, glycosomal 5693 1.2.1.12 | Details
100 3B20 1 A, B, O, P, Q, R Glyceraldehyde 3-phosphate dehydrogenase (NADP+) 32046
101 4QX6 1 A, B, C, D Glyceraldehyde 3-phosphate dehydrogenase 1311
102 3L0D 1 A, B Glyceraldehyde 3-phosphate dehydrogenase 38323 1.2.1.12 | Details
103 1CER 1 A, B, C, D, O, P, Q, R HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 271 1.2.1.12 | Details
104 1ZNQ 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase, liver 9606 1.2.1.12 | Details
105 4IQ8 1 A Glyceraldehyde-3-phosphate dehydrogenase 3 4932 1.2.1.12 | Details
106 5T73 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
107 4Z0H 1 O, R Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic 3702 1.2.1.12 | Details
108 3KSZ 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
109 1NBO 1 A, B, O glyceraldehyde-3-phosphate dehydrogenase A 3562 1.2.1.13 | Details
110 1IHX 1 A, B, C, D GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 150436 1.2.1.12 | Details
111 1I32 1 A, B, C, D, E, F GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 5665 1.2.1.12 | Details
112 4DIB 1 A, B, C, D, E, F, G, H Glyceraldehyde 3-phosphate dehydrogenase 1392
113 6IEP 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
114 5JYA 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
115 3LC2 1 O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
116 2PKR 1 A, B, C, D, H, I, L, M, O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase Aor 3562 1.2.1.13 | Details
117 5DDI 1 P, R, S Glyceraldehyde-3-phosphate dehydrogenase 9823 1.2.1.12 | Details
118 4MVJ 1 A, B, C, K, N Glyceraldehyde-3-phosphate dehydrogenase A 562 1.2.1.12 | Details
119 4MVJ 2 D, L Glyceraldehyde-3-phosphate dehydrogenase A 562 1.2.1.12 | Details
120 4MVJ 3 E Glyceraldehyde-3-phosphate Dehydrogenase A 562 1.2.1.12 | Details
121 4MVJ 4 F, J, O Glyceraldehyde-3-phosphate Dehydrogenase A 562 1.2.1.12 | Details
122 4MVJ 5 G Glyceraldehyde-3-phosphate Dehydrogenase A 562 1.2.1.12 | Details
123 4MVJ 6 H Glyceraldehyde-3-phosphate Dehydrogenase A 562 1.2.1.12 | Details
124 4MVJ 7 I Glyceraldehyde-3-phosphate Dehydrogenase A 562 1.2.1.12 | Details
125 4MVJ 8 M Glyceraldehyde-3-phosphate Dehydrogenase A 562 1.2.1.12 | Details
126 4MVJ 9 P Glyceraldehyde-3-phosphate Dehydrogenase A 562 1.2.1.12 | Details
127 1QXS 1 A, B, C, D Glyceraldehyde 3-phosphate dehydrogenase, glycosomal 5693 1.2.1.12 | Details
128 1VC2 1 A Glyceraldehyde 3-Phosphate Dehydrogenase 274 1.2.1.12 | Details
129 2X0N 1 A, B, O, P, Q, R GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL 5691 1.2.1.12 | Details
130 1GYP 1 A, B, C, D GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 5665 1.2.1.12 | Details
131 1IHY 1 A, B, C, D GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 150436 1.2.1.12 | Details
132 1YWG 1 O, P, Q, R glyceraldehyde-3-phosphate dehydrogenase 5833 1.2.1.12 | Details
133 5JYF 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
134 3K2B 1 A, B, C, D, E, F, G, H, O, Q Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 3702 1.2.1.13 | Details
135 1A7K 1 A, B, C, D GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE ONE BOUND NAD AND TWO BOUND PHOSPHATES PER MONOMER 5665 1.2.1.12 | Details
136 4GPD 1 1, 2, 3, 4 APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 6706 1.2.1.12 | Details
137 3RVD 1 A, B, C, D, E, F, G, H, O, Q Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 3702 1.2.1.13 | Details
138 1I33 1 A, B, C, D, E, F GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 5665 1.2.1.12 | Details
139 6ADE 1 A, B, C Glyceraldehyde-3-phosphate dehydrogenase 9606 1.2.1.12 | Details
140 2HKI 1 A Glyceraldehyde-3-phosphate dehydrogenase A, chloroplast 3562 1.2.1.13 | Details
141 1JN0 1 A, B, O GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A tetramer GAPDH 2 3562 1.2.1.13 | Details
142 5V8X 1 A, B, C, D Glyceraldehyde-3-phosphate dehydrogenase 1311 1.2.1 | Details
143 3VAZ 1 A, B, O, P, Q, R Glyceraldehyde-3-phosphate dehydrogenase 1 1280 1.2.1.12 | Details
144 2XF8 1 A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE IN COVALENT COMPLEX WITH A COFACTOR ANALOG THROUGH ITS CATALYTIC CYSTEINE (C149) 562 1.2.1.72 | Details
145 3E6A 1 A, B, C, O Glyceraldehyde-3-phosphate dehydrogenase, cytosolic ligand binding 4530 1.2.1.12 | Details
146 3B1K 1 A, B, G, H Glyceraldehyde 3-phosphate dehydrogenase (NADP+) 32046
147 2PKQ 1 O, Q, T Glyceraldehyde-3-phosphate dehydrogenase B 3562 1.2.1.13 | Details
148 2PKQ 2 P, R, S Glyceraldehyde-3-phosphate dehydrogenase A 3562 1.2.1.13 | Details
149 3GPD 1 G, R D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 9606 1.2.1.12 | Details
150 1GYQ 1 A, B, C, D PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE) 5665 1.2.1.12 | Details
151 1GPD 1 G, R D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 6706 1.2.1.12 | Details