MolNFT v1 · #108864 · protein

Ampr effector binding domain from citrobacter freundii bound to udp- murnac-pentapeptide

4WKM · Lysr family transcriptional regulator: “Ampr effector binding domain from citrobacter freundii bound to udp- murnac-pentapeptide”. X-ray diffraction, 2 ligands (API, MUB), 20 pockets (best druggability 0.73). MolNFT v1 #108864 on…

PDB: 4WKM
Type: protein
Length: 1,601 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysr family transcriptional regulator; Ala-fga-api-dal-dal
UniProt: K8QNC4
Ligands: API, MUB
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysr family transcriptional regulator	protein	197	36% helix, 29% strand	K8QNC4
B, C, D, E, F, G, H	Lysr family transcriptional regulator	protein	196	34% helix, 28% strand	K8QNC4
I, J, K, L, M, N, O, P	Ala-fga-api-dal-dal	protein	4	0% helix, 0% strand	—

Ligands and binding sites

API · 2,6-diaminopimelic acid · ligand · 8 copies · chains A, B, I, J, C, D, K, L, E, F, M, N, G, H, O, P
MUB · N-acetyl-alpha-muramic acid · ligand · 8 copies · chains A, B, I, J, C, D, K, L, E, M, F, N, G, O, H, P
GOL · Glycerol · additive · 7 copies · chains A, I, C, K, D, L, E, M, F, N, G, O, H, P

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

Pockets

20 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	919	0.73	0.77	68	empty
2	445	0.59	0.75	41	empty
3	218	0.56	0.79	28	API
4	183	0.53	0.79	29	API
5	162	0.53	0.80	21	empty

Interfaces

18 interfaces between chains.

G–H · 1100 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1061 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1050 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1049 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 533 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 covalent, 16 d-amino, 8 modified (covalent ligand, D-amino acid, nonstandard).

Compared structures

4WKM · AmpR effector binding domain from Citrobacter freundii bound to UDP-MurNAc-pentapeptide · the same entry in another collection · chain B against B, 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 K8QNC4
Elsewhere: RCSB PDB 4WKM · PDBe 4WKM · UniProt K8QNC4

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