MolNFT v1 · #180022 · protein

Crystal structure of ispd from mycobacterium paratuberculosis

7KMW · 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: “Crystal structure of ispd from mycobacterium paratuberculosis”. X-ray diffraction, 9 pockets (best druggability 0.83). MolNFT v1 #180022 on GenesisL1: 3D structure, binding…

PDB: 7KMW
Type: protein
Length: 856 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
EC: 2.7.7.60
UniProt: Q743W5
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)	protein	220	38% helix, 24% strand	Q743W5
B	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)	protein	214	37% helix, 24% strand	Q743W5
C	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)	protein	208	38% helix, 25% strand	Q743W5
D	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)	protein	214	37% helix, 24% strand	Q743W5

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, D, C

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

Pockets

9 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	506	0.83	0.89	35	EDO
2	405	0.82	0.90	37	empty
3	378	0.67	0.80	57	EDO
4	426	0.58	0.74	49	EDO
5	264	0.57	0.78	32	empty

Interfaces

6 interfaces between chains.

C–D · 1802 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 1716 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 485 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 316 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 272 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7KMW · Crystal structure of IspD from Mycobacterium paratuberculosis · the same entry in another collection · chain D against D, TM-score 1.00
Q743W5 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 4-phosphate… · a predicted model of the same protein · chain D against A, TM-score 0.96

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 Q743W5
Elsewhere: RCSB PDB 7KMW · PDBe 7KMW · UniProt Q743W5

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