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Crystallographic Analysis of Nucleoside Diphosphate Kinase (NDK) from Aspergillus Flavus
Analyse Crystallographic Analysis of Nucleoside Diphosphate Kinase (NDK) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K3H
- Type
- protein
- Length
- 3,610 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.179
- Source
- Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 /…
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- B8NQF0
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.179 · 8 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, I, K, M, Q, R, O, T | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 47% helix, 16% strand | B8NQF0 |
| B, E, H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 47% helix, 16% strand | B8NQF0 |
| C, F, G, J, W | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 150 | 49% helix, 16% strand | B8NQF0 |
| L | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 46% helix, 16% strand | B8NQF0 |
| N | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 139 | 40% helix, 17% strand | B8NQF0 |
| U | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 150 | 47% helix, 16% strand | B8NQF0 |
| V, X, P | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 150 | 45% helix, 16% strand | B8NQF0 |
| S | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 149 | 46% helix, 16% strand | B8NQF0 |
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 | 640 | 0.82 | 0.86 | 93 | empty |
| 2 | 311 | 0.79 | 0.90 | 41 | empty |
| 3 | 274 | 0.79 | 0.91 | 41 | empty |
| 4 | 266 | 0.78 | 0.90 | 39 | empty |
| 5 | 294 | 0.78 | 0.90 | 42 | empty |
Interfaces
55 interfaces between chains.
- W–X · 1018 Ų buried · 19 hydrogen bonds · protein-protein
- M–N · 1003 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1002 Ų buried · 22 hydrogen bonds · protein-protein
- Q–R · 994 Ų buried · 22 hydrogen bonds · protein-protein
- S–T · 990 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6K3H · Crystallographic analysis of nucleoside diphosphate kinase (ndk) from aspergillus flavus · 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 B8NQF0
- Elsewhere: RCSB PDB 6K3H · PDBe 6K3H · UniProt B8NQF0
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