MolNFT v1 · #18354 · protein

Rmlc (dtdp-6-deoxy-D-xylo-4-hexulose 3,5-EPIMERASE)STRUCTURE from mycobacterium tuberculosis and inhibitor design. the apo structure.

1PM7 · Rfbc: “Rmlc (dtdp-6-deoxy-D-xylo-4-hexulose 3,5-EPIMERASE)STRUCTURE from mycobacterium tuberculosis and inhibitor…”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #18354 on GenesisL1: 3D structure, binding sites…

PDB: 1PM7
Type: protein
Length: 398 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rfbc
EC: 5.1.3.13
UniProt: O06330
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Rfbc (EC 5.1.3.13)	protein	199	14% helix, 40% strand	O06330

Ligands and binding sites

ACT · Acetate ion · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	283	0.68	0.83	28	ACT
2	273	0.66	0.83	26	ACT
3	54	0.48	0.85	19	GOL
4	67	0.33	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 1535 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

1PM7 · RmlC (dTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE)STRUCTURE FROM MYCOBACTERIUM… · 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 O06330
Elsewhere: RCSB PDB 1PM7 · PDBe 1PM7 · UniProt O06330

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