MolNFT v1 · #114255 · protein

Crystal structure of complement C5 in complex with SKY59

5B71 · SKY59 Fab light chain: “Crystal structure of complement C5 in complex with SKY59”. X-ray diffraction, 12 pockets (best druggability 0.55). MolNFT v1 #114255 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B71
Type: protein
Length: 1,057 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SKY59 Fab light chain; SKY59 Fab heavy chain; Complement C5 beta chain
UniProt: P01031
Pockets: 12 · best druggability 0.55

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SKY59 Fab light chain	protein	217	8% helix, 49% strand	—
B	SKY59 Fab heavy chain	protein	222	5% helix, 49% strand	—
C	SKY59 Fab light chain	protein	214	6% helix, 50% strand	—
D	SKY59 Fab heavy chain	protein	219	4% helix, 50% strand	—
E	Complement C5 beta chain	protein	93	0% helix, 63% strand	P01031
F	Complement C5 beta chain	protein	92	0% helix, 58% strand	P01031

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	379	0.55	0.74	46	empty
2	352	0.54	0.74	45	empty
3	208	0.46	0.74	23	empty
4	97	0.44	0.79	21	empty
5	195	0.42	0.73	31	empty

Interfaces

8 interfaces between chains.

A–B · 2069 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1957 Å² buried · 18 hydrogen bonds · protein-protein
B–E · 634 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 626 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 224 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5B71 · Crystal structure of complement C5 in complex with SKY59 · the same entry in another collection · chain F against F, TM-score 1.00
P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 P01031
Elsewhere: RCSB PDB 5B71 · PDBe 5B71 · UniProt P01031

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