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Crystal structure of D-cycloserine synthetase dcsg

Analyse Crystal structure of D-cycloserine synthetase dcsg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JIL
Type: protein
Length: 1,191 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cycloserine biosynthesis protein dcsg
EC: 6.3.3.5
UniProt: D2Z030
Ligands: ADP, MG
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cycloserine biosynthesis protein dcsg (EC 6.3.3.5)	protein	297	39% helix, 25% strand	D2Z030
B, C, D	Cycloserine biosynthesis protein dcsg (EC 6.3.3.5)	protein	298	39% helix, 25% strand	D2Z030

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
TLA · L(+)-tartaric acid · additive · 10 copies · chains A, B, C, D

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

Pockets

14 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	247	0.84	0.96	40	TLA, ADP, MG
2	227	0.82	0.95	36	TLA, ADP, MG
3	278	0.81	0.93	43	TLA, ADP, MG
4	277	0.81	0.93	42	TLA, ADP, MG
5	616	0.80	0.85	81	empty

Interfaces

5 interfaces between chains.

A–B · 607 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 602 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 486 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 307 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 284 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 modified (engineered).

Compared structures

6JIL · Crystal structure of D-cycloserine synthetase DcsG · the same entry in another collection · chain D against D, TM-score 1.00
D2Z030 · AlphaFold monomer V2.0 prediction for cycloserine biosynthesis protein dcsg (D2Z030) · 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 D2Z030
Elsewhere: RCSB PDB 6JIL · PDBe 6JIL · UniProt D2Z030

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