MolNFT v1 · #154211 · protein

Crystallographic analysis of nucleoside diphosphate kinase (ndk) from aspergillus flavus

6K3H: “Crystallographic analysis of nucleoside diphosphate kinase (ndk) from aspergillus flavus”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #154211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6K3H
Type: protein
Length: 3,610 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: B8NQF0
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 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.

Pocket	Volume (Å³)	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 Å² buried · 19 hydrogen bonds · protein-protein
M–N · 1003 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1002 Å² buried · 22 hydrogen bonds · protein-protein
Q–R · 994 Å² buried · 22 hydrogen bonds · protein-protein
S–T · 990 Å² 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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