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 3000
95 % 5 6 3136 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.6
PDBFlex
90 % 5 7 2425
70 % 5 12 1151
50 % 95 145 75
40 % 95 145 97
30 % 95 145 110

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