MolNFT v1 · #114233 · protein

Crystal structure of cytidine monophosphate hydroxymethylase mila with cmp

5B6D · Cmp 5-hydroxymethylase: “Crystal structure of cytidine monophosphate hydroxymethylase mila with cmp”. X-ray diffraction, 1 ligand (C5P), 8 pockets (best druggability 0.76). MolNFT v1 #114233 on GenesisL1: 3D structure, binding sites…

PDB: 5B6D
Type: protein
Length: 633 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cmp 5-hydroxymethylase
UniProt: B4Y380
Ligands: C5P
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cmp 5-hydroxymethylase	protein	316	48% helix, 18% strand	B4Y380
B	Cmp 5-hydroxymethylase	protein	317	48% helix, 18% strand	B4Y380

Ligands and binding sites

C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B

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

Pockets

8 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	527	0.76	0.84	50	C5P
2	566	0.76	0.83	49	C5P
3	169	0.49	0.77	24	empty
4	102	0.41	0.77	16	empty
5	98	0.39	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 2232 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

5B6D · Crystal Structure of cytidine monophosphate hydroxymethylase MilA with CMP · 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 B4Y380
Elsewhere: RCSB PDB 5B6D · PDBe 5B6D · UniProt B4Y380

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