MolNFT v1 · #74030 · protein

Structure of mtb apo 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (ispd)

3OKR · 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: “Structure of mtb apo 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (ispd)”. X-ray diffraction, 7 pockets (best druggability 0.80). MolNFT v1 #74030 on GenesisL1: 3D…

PDB: 3OKR
Type: protein
Length: 817 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; Heptamer peptide
EC: 2.7.7.60
UniProt: P96864
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)	protein	203	38% helix, 25% strand	P96864
B	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)	protein	208	37% helix, 23% strand	P96864
C	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)	protein	194	32% helix, 25% strand	P96864
D	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)	protein	205	34% helix, 25% strand	P96864
F	Heptamer peptide	protein	7	0% helix, 43% strand	—

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	534	0.80	0.86	35	empty
2	539	0.78	0.85	37	empty
3	819	0.66	0.73	64	empty
4	242	0.56	0.78	38	empty
5	89	0.47	0.81	15	empty

Interfaces

5 interfaces between chains.

A–B · 1627 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1604 Å² buried · 30 hydrogen bonds · protein-protein
D–F · 213 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 125 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 70 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3OKR · Structure of Mtb apo 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) · 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 P96864
Elsewhere: RCSB PDB 3OKR · PDBe 3OKR · UniProt P96864

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