MolNFT v1 · #109572 · protein

Crystal structure of S. aureus tarm in complex with udp

4X6L: “Crystal structure of S. aureus tarm in complex with udp”. X-ray diffraction, 1 ligand (UDP), 18 pockets (best druggability 0.80). MolNFT v1 #109572 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X6L
Type: protein
Length: 1,972 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tarm
UniProt: H0AM96
Ligands: UDP
Pockets: 18 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Tarm	protein	493	34% helix, 26% strand	H0AM96

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 3 copies · chains A, B, C

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

Pockets

18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	651	0.80	0.84	78	empty
2	641	0.79	0.84	74	UDP
3	643	0.79	0.84	71	UDP
4	647	0.78	0.84	75	UDP
5	915	0.69	0.75	86	empty

Interfaces

2 interfaces between chains.

A–D · 376 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 370 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4X6L · Crystal structure of S. aureus TarM in complex with UDP · 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 H0AM96
Elsewhere: RCSB PDB 4X6L · PDBe 4X6L · UniProt H0AM96

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