MolNFT v1 · #173525 · protein

Cryo-EM structure of complement C4B in complex with nanobody B5

7B2P · Complement C4 beta chain: “Cryo-EM structure of complement C4B in complex with nanobody B5”. Electron microscopy, 1 ligand (NAG), 19 pockets (best druggability 0.75). MolNFT v1 #173525 on GenesisL1: 3D structure, binding sites and…

PDB: 7B2P
Type: protein
Length: 1,509 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C4 beta chain; Complement C4 alpha chain; Complement C4 gamma chain; Nanobody…
UniProt: P0C0L4
Ligands: NAG
Pockets: 19 · best druggability 0.75

Structure

electron microscopy · 4 distinct chains · 16% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement C4 beta chain	protein	650	7% helix, 43% strand	P0C0L4
B	Complement C4 alpha chain	protein	610	30% helix, 24% strand	P0C0L4
C	Complement C4 gamma chain	protein	130	6% helix, 41% strand	P0C0L4
D	Nanobody B5	protein	119	3% helix, 43% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B

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

Pockets

19 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	1166	0.75	0.78	96	empty
2	864	0.72	0.77	88	empty
3	230	0.66	0.84	39	empty
4	267	0.65	0.82	41	empty
5	262	0.63	0.81	46	empty

Interfaces

5 interfaces between chains.

A–B · 5148 Å² buried · 91 hydrogen bonds · protein-protein
B–C · 2407 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 822 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 789 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 118 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

7B2P · Cryo-EM structure of complement C4b in complex with nanobody B5 · the same entry in another collection · chain A against A, TM-score 1.00
P0C0L4 · AlphaFold monomer V2.0 prediction for complement C4-a (P0C0L4) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P0C0L4
Elsewhere: RCSB PDB 7B2P · PDBe 7B2P · UniProt P0C0L4

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