MolNFT v1 · #37126 · protein

Crystal structure of mouse cytidine deaminase complexed with cytidine

2FR6: “Crystal structure of mouse cytidine deaminase complexed with cytidine”. X-ray diffraction, 5 ligands (CTN, URI, ZN), 7 pockets (best druggability 0.81). MolNFT v1 #37126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2FR6
Type: protein
Length: 543 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytidine deaminase
EC: 3.5.4.5
UniProt: P56389
Ligands: CTN, URI, ZN, SO4, NH3
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Cytidine deaminase (EC 3.5.4.5)	protein	137	34% helix, 24% strand	P56389
B	Cytidine deaminase (EC 3.5.4.5)	protein	135	36% helix, 24% strand	P56389
C	Cytidine deaminase (EC 3.5.4.5)	protein	134	34% helix, 25% strand	P56389

Ligands and binding sites

CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 3 copies · chains A, B, C, D
URI · Uridine · ligand · chains A, B, D
ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
SO4 · Sulfate ion · ion · chains A
NH3 · Ammonia · ion · chains A, B

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

Pockets

7 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	199	0.81	0.95	30	empty
2	97	0.78	0.98	24	CTN
3	97	0.78	0.98	24	CTN
4	91	0.77	0.98	24	CTN
5	83	0.77	0.98	24	URI, NH3

Interfaces

6 interfaces between chains.

A–D · 1321 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1256 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 879 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 852 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 475 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2FR6 · Crystal Structure of Mouse Cytidine Deaminase Complexed with Cytidine · the same entry in another collection · chain D against D, TM-score 1.00
P56389 · AlphaFold monomer V2.0 prediction for cytidine deaminase (P56389) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P56389
Elsewhere: RCSB PDB 2FR6 · PDBe 2FR6 · UniProt P56389

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