MolNFT v1 · #85084 · protein

Ykud from B.SUBTILIS

4A1I · Putative L, D-transpeptidase ykud: “Ykud from B.SUBTILIS”. X-ray diffraction, 3 ligands (CD, SO4, CL), 14 pockets (best druggability 0.83). MolNFT v1 #85084 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4A1I
Type: protein
Length: 1,316 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative L, D-transpeptidase ykud
EC: 2.-.-.-
UniProt: O34816
Ligands: CD, SO4, CL
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Putative L, D-transpeptidase ykud (EC 2.-.-.-)	protein	165	22% helix, 35% strand	O34816
E, F, G, H	Putative L, D-transpeptidase ykud (EC 2.-.-.-)	protein	164	24% helix, 34% strand	O34816

Ligands and binding sites

CD · Cadmium ion · metal · 8 copies · chains A, H, B, C, F, D, E, G
SO4 · Sulfate ion · ion · 22 copies · chains A, H, D, B, C, F, E, G
CL · Chloride ion · ion · 8 copies · chains A, H, B, C, F, D, E, G

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

Pockets

14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.83	0.85	104	empty
2	306	0.78	0.89	60	empty
3	495	0.68	0.79	63	empty
4	125	0.68	0.90	36	SO4
5	353	0.64	0.79	53	SO4, CD, CL

Interfaces

14 interfaces between chains.

C–G · 1010 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 993 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 981 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 976 Å² buried · 18 hydrogen bonds · protein-protein
A–H · 961 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4A1I · ykud from B.subtilis · the same entry in another collection · chain H against H, TM-score 1.00
O34816 · AlphaFold monomer V2.0 prediction for putative L,D-transpeptidase ykud (O34816) · a predicted model of the same protein · chain A 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 O34816
Elsewhere: RCSB PDB 4A1I · PDBe 4A1I · UniProt O34816

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