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Crystal structure of dcmp deaminase from the cyanophage S-TIM5 in complex with dcmp and dump

Analyse Crystal structure of dcmp deaminase from the cyanophage S-TIM5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P9C
Type: protein
Length: 1,629 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxycytidylate deaminase
UniProt: H6WFU3
Ligands: DCM, DU, ZN
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, J, K	Deoxycytidylate deaminase	protein	136	32% helix, 23% strand	H6WFU3
H, I, L	Deoxycytidylate deaminase	protein	135	32% helix, 23% strand	H6WFU3

Ligands and binding sites

DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 12 copies · chains A, K, L, B, G, H, C, I, D, E, J, F
DU · 2'-deoxyuridine-5'-monophosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1029	0.71	0.75	108	DCM
2	395	0.71	0.82	54	DU
3	431	0.70	0.81	56	DU
4	400	0.70	0.81	55	DU
5	782	0.68	0.75	93	DCM

Interfaces

21 interfaces between chains.

B–G · 1282 Å² buried · 13 hydrogen bonds · protein-protein
C–H · 1270 Å² buried · 15 hydrogen bonds · protein-protein
F–J · 1260 Å² buried · 17 hydrogen bonds · protein-protein
A–L · 1244 Å² buried · 17 hydrogen bonds · protein-protein
E–K · 1240 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4P9C · Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dCMP and… · 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 H6WFU3
Elsewhere: RCSB PDB 4P9C · PDBe 4P9C · UniProt H6WFU3

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