MolNFT v1 · #87427 · protein

The N-terminal domain of the streptococcus pyogenes pilus tip adhesin cpa

4C0Z · Ancillary protein 2: “The N-terminal domain of the streptococcus pyogenes pilus tip adhesin cpa”. X-ray diffraction, 3 ligands (SPD, CL, PO4), 20 pockets (best druggability 0.82). MolNFT v1 #87427 on GenesisL1: 3D structure, binding…

PDB: 4C0Z
Type: protein
Length: 2,488 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ancillary protein 2
UniProt: S5FV19
Ligands: SPD, CL, PO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 31% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, H	Ancillary protein 2	protein	208	30% helix, 19% strand	S5FV19
B	Ancillary protein 2	protein	208	32% helix, 19% strand	S5FV19
C	Ancillary protein 2	protein	205	31% helix, 19% strand	S5FV19
E	Ancillary protein 2	protein	206	31% helix, 19% strand	S5FV19
F, L	Ancillary protein 2	protein	209	30% helix, 19% strand	S5FV19
G, I, J	Ancillary protein 2	protein	207	30% helix, 19% strand	S5FV19
K	Ancillary protein 2	protein	206	31% helix, 18% strand	S5FV19

Ligands and binding sites

SPD · Spermidine · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
CL · Chloride ion · ion · 14 copies · chains A, B, H, C, D, E, F, G, I, J, K, L
PO4 · Phosphate ion · ion · 3 copies · chains B, C, J, F
GOL · Glycerol · additive · 3 copies · chains C, D, I, 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	999	0.82	0.83	117	empty
2	345	0.79	0.89	39	empty
3	283	0.76	0.88	48	empty
4	313	0.76	0.87	52	empty
5	490	0.75	0.83	53	empty

Interfaces

18 interfaces between chains.

E–F · 1262 Å² buried · 13 hydrogen bonds · protein-protein
K–L · 1232 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1225 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1218 Å² buried · 13 hydrogen bonds · protein-protein
I–J · 1214 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 covalent (covalent ligand).

Compared structures

4C0Z · The N-terminal domain of the Streptococcus pyogenes pilus tip adhesin Cpa · the same entry in another collection · chain L against L, 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 S5FV19
Elsewhere: RCSB PDB 4C0Z · PDBe 4C0Z · UniProt S5FV19

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