MolNFT v1 · #181314 · protein

Complex of Fab 2/1.12 with domain 3 of P. berghei HAP2

7LR4 · D3_2/1.12 Fab heavy chain: “Complex of Fab 2/1.12 with domain 3 of P. berghei HAP2”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.74). MolNFT v1 #181314 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7LR4
Type: protein
Length: 1,057 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D3_2/1.12 Fab heavy chain; D3_2/1.12 Fab light chain; Hapless 2
UniProt: Q4YCF6
Ligands: SO4
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	D3_2/1.12 Fab heavy chain	protein	218	7% helix, 49% strand	—
L	D3_2/1.12 Fab light chain	protein	213	5% helix, 53% strand	—
A	D3_2/1.12 Fab heavy chain	protein	216	6% helix, 49% strand	—
B	D3_2/1.12 Fab light chain	protein	212	6% helix, 50% strand	—
C	Hapless 2	protein	99	0% helix, 57% strand	Q4YCF6
D	Hapless 2	protein	99	0% helix, 53% strand	Q4YCF6

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains H, D, A, C, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains H

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	868	0.74	0.78	85	empty
2	256	0.63	0.81	42	SO4
3	255	0.63	0.81	37	SO4
4	331	0.54	0.75	47	empty
5	332	0.54	0.74	55	empty

Interfaces

9 interfaces between chains.

H–L · 1871 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1723 Å² buried · 14 hydrogen bonds · protein-protein
H–D · 442 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 428 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 419 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

7LR4 · Complex of Fab 2/1.12 with domain 3 of P. berghei HAP2 · the same entry in another collection · chain D against D, TM-score 1.00
Q4YCF6 · AlphaFold monomer V2.0 prediction for hapless 2 (Q4YCF6) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 Q4YCF6
Elsewhere: RCSB PDB 7LR4 · PDBe 7LR4 · UniProt Q4YCF6

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