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 2487
95 % 5 6 3140 Flexibility: Low
Max RMSD: 1.0, Avg RMSD: 0.6
PDBFlex
90 % 5 7 2354
70 % 5 12 1104
50 % 90 139 74
40 % 90 139 95
30 % 90 139 107

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