MolNFT v1 · #139241 · protein

Crystal structure of hldc from burkholderia pseudomallei

5X9Q · Putative cytidylyltransferase: “Crystal structure of hldc from burkholderia pseudomallei”. X-ray diffraction, 9 pockets (best druggability 0.71). MolNFT v1 #139241 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X9Q
Type: protein
Length: 632 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative cytidylyltransferase
UniProt: Q63XZ4
Pockets: 9 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Putative cytidylyltransferase	protein	158	45% helix, 19% strand	Q63XZ4

Ligands and binding sites

MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	303	0.71	0.84	38	MES
2	444	0.71	0.81	40	MES
3	346	0.61	0.77	31	empty
4	376	0.60	0.76	36	empty
5	406	0.59	0.75	39	empty

Interfaces

5 interfaces between chains.

A–B · 1407 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1281 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 363 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 346 Å² buried · 1 hydrogen bond · protein-protein
B–C · 309 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5X9Q · Crystal structure of HldC from Burkholderia pseudomallei · 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 Q63XZ4
Elsewhere: RCSB PDB 5X9Q · PDBe 5X9Q · UniProt Q63XZ4

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