MolNFT v1 · #182206 · protein
Trypanosoma cruzi nucleoside diphosphate kinase 1 form a quinary multihexameric structure
7MK0: “Trypanosoma cruzi nucleoside diphosphate kinase 1 form a quinary multihexameric structure”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #182206 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MK0
- Type
- protein
- Length
- 3,624 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- A0A2V2WVR0
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 42% helix, 15% strand | A0A2V2WVR0 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.88 | 0.90 | 115 | empty |
| 2 | 398 | 0.84 | 0.92 | 52 | empty |
| 3 | 546 | 0.84 | 0.89 | 60 | empty |
| 4 | 369 | 0.84 | 0.93 | 59 | empty |
| 5 | 321 | 0.83 | 0.93 | 51 | empty |
Interfaces
61 interfaces between chains.
- A–D · 1330 Ų buried · 28 hydrogen bonds · protein-protein
- T–W · 1293 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 1266 Ų buried · 25 hydrogen bonds · protein-protein
- G–J · 1233 Ų buried · 19 hydrogen bonds · protein-protein
- M–P · 1195 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7MK0 · Trypanosoma cruzi Nucleoside Diphosphate Kinase 1 form a quinary multihexameric structure · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A2V2WVR0
- Elsewhere: RCSB PDB 7MK0 · PDBe 7MK0 · UniProt A0A2V2WVR0
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