MolNFT v1 · #142767 · protein

Crystal structure of nucleoside diphosphate kinase from pseudomonas aeruginosa at 3.55 a resolution.

6AES: “Crystal structure of nucleoside diphosphate kinase from pseudomonas aeruginosa at 3.55 a resolution.”. X-ray diffraction, 11 pockets (best druggability 0.84). MolNFT v1 #142767 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6AES
Type: protein
Length: 1,144 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase
EC: 2.7.4.6
UniProt: A0A1G5LIK5
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	143	45% helix, 20% strand	A0A1G5LIK5

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1111	0.84	0.85	87	empty
2	1077	0.84	0.84	86	empty
3	730	0.71	0.77	62	empty
4	478	0.69	0.80	33	empty
5	206	0.57	0.80	35	empty

Interfaces

16 interfaces between chains.

G–H · 1091 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1087 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 1059 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1017 Å² buried · 21 hydrogen bonds · protein-protein
A–E · 494 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6AES · Crystal structure of Nucleoside diphosphate kinase from Pseudomonas aeruginosa at 3.55 A… · 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 A0A1G5LIK5
Elsewhere: RCSB PDB 6AES · PDBe 6AES · UniProt A0A1G5LIK5

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