MolNFT v1 · #180413 · protein

Psabc from streptococcus pneumoniae in complex with Fab

7KYP · Manganese ABC transporter, ATP-binding protein: “Psabc from streptococcus pneumoniae in complex with Fab”. X-ray diffraction, 2 ligands (MA4, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #180413 on GenesisL1: 3D structure…

PDB: 7KYP
Type: protein
Length: 4,083 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Manganese ABC transporter, ATP-binding protein; Manganese ABC transporter, permease…
UniProt: A0A0H2ZNF3, A0A0H2ZPI2
Ligands: MA4, PO4
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 12 distinct chains · 66% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, K	Manganese ABC transporter, ATP-binding protein	protein	236	35% helix, 24% strand	A0A0H2ZNF3
B, L	Manganese ABC transporter, permease protein	protein	278	83% helix, 0% strand	A0A0H2ZPI2
C	Manganese ABC transporter, ATP-binding protein	protein	232	40% helix, 25% strand	A0A0H2ZNF3
D	Manganese ABC transporter, permease protein	protein	272	86% helix, 0% strand	A0A0H2ZPI2
F	Manganese ABC transporter, permease protein	protein	290	80% helix, 0% strand	A0A0H2ZPI2
G	Manganese ABC transporter, ATP-binding protein	protein	230	38% helix, 26% strand	A0A0H2ZNF3
H	Manganese ABC transporter, permease protein	protein	272	83% helix, 0% strand	A0A0H2ZPI2
I, O	Manganese ABC transporter, ATP-binding protein	protein	234	40% helix, 23% strand	A0A0H2ZNF3
J	Manganese ABC transporter, permease protein	protein	274	83% helix, 0% strand	A0A0H2ZPI2
M	Manganese ABC transporter, ATP-binding protein	protein	233	36% helix, 25% strand	A0A0H2ZNF3
N	Manganese ABC transporter, permease protein	protein	277	81% helix, 0% strand	A0A0H2ZPI2
P	Manganese ABC transporter, permease protein	protein	271	84% helix, 0% strand	A0A0H2ZPI2

Ligands and binding sites

MA4 · Cyclohexyl-hexyl-beta-D-maltoside · ligand · 4 copies · chains B, C, F, L, I, N
PO4 · Phosphate ion · ion · 8 copies · chains A, C, E, G, I, K, M, O

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	115	0.79	0.98	29	empty
2	984	0.78	0.80	106	empty
3	97	0.77	0.98	22	empty
4	106	0.77	0.97	30	empty
5	503	0.76	0.84	54	empty

Interfaces

33 interfaces between chains.

F–H · 2141 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 2136 Å² buried · 8 hydrogen bonds · protein-protein
J–L · 2106 Å² buried · 4 hydrogen bonds · protein-protein
N–P · 2092 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 1529 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7KYP · PsaBC from Streptococcus pneumoniae in complex with Fab · the same entry in another collection · chain H against H, 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 A0A0H2ZNF3
Every structure of UniProt A0A0H2ZPI2
Elsewhere: RCSB PDB 7KYP · PDBe 7KYP · UniProt A0A0H2ZNF3 · UniProt A0A0H2ZPI2

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