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 3129
95 % 5 6 3243 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.6
PDBFlex
90 % 5 7 2504
70 % 5 12 1191
50 % 97 148 77
40 % 97 148 99
30 % 97 148 111

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