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Nerve growth factor in complex with Fab from mouse mab 911

Analyse Nerve growth factor in complex with Fab from mouse mab 911 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EDX
Type: protein
Length: 1,063 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-nerve growth factor; Light chain of Fab of murine anti-ngf; Heavy chain of Fab of…
UniProt: P01138
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
W	Beta-nerve growth factor	protein	102	0% helix, 64% strand	P01138
A, L	Light chain of Fab of murine anti-ngf	protein	214	7% helix, 52% strand	—
B, H	Heavy chain of Fab of murine anti-ngf	protein	216	4% helix, 54% strand	—
V	Beta-nerve growth factor	protein	101	0% helix, 64% strand	P01138

Pockets

13 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	83	0.75	0.97	30	empty
2	648	0.65	0.75	75	empty
3	158	0.61	0.84	27	empty
4	548	0.61	0.74	70	empty
5	157	0.60	0.84	29	empty

Interfaces

11 interfaces between chains.

L–H · 1964 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1939 Å² buried · 11 hydrogen bonds · protein-protein
W–V · 1664 Å² buried · 17 hydrogen bonds · protein-protein
W–B · 582 Å² buried · 8 hydrogen bonds · protein-protein
V–H · 571 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4EDX · Nerve Growth Factor in Complex with Fab from mouse mAb 911 · the same entry in another collection · chain H against H, TM-score 1.00
P01138 · AlphaFold monomer V2.0 prediction for beta-nerve growth factor (P01138) · a predicted model of the same protein · chain V against A, TM-score 0.90

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 P01138
Elsewhere: RCSB PDB 4EDX · PDBe 4EDX · UniProt P01138

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