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Crystal structure of chimeric avidin

Analyse Crystal structure of chimeric avidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MM0
Type: protein
Length: 1,404 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin, avidin-related protein 4/5
UniProt: P02701, P56734
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 8 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Avidin, avidin-related protein 4/5	protein	115	8% helix, 50% strand	P02701, P56734
C	Avidin, avidin-related protein 4/5	protein	118	8% helix, 49% strand	P02701, P56734
D, K	Avidin, avidin-related protein 4/5	protein	119	5% helix, 52% strand	P02701, P56734
E	Avidin, avidin-related protein 4/5	protein	116	3% helix, 50% strand	P02701, P56734
F, I	Avidin, avidin-related protein 4/5	protein	118	3% helix, 51% strand	P02701, P56734
G	Avidin, avidin-related protein 4/5	protein	117	5% helix, 50% strand	P02701, P56734
H, M	Avidin, avidin-related protein 4/5	protein	116	8% helix, 51% strand	P02701, P56734
N	Avidin, avidin-related protein 4/5	protein	117	8% helix, 50% strand	P02701, P56734

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	105	0.72	0.94	26	empty
2	73	0.71	0.95	19	empty
3	479	0.69	0.80	58	empty
4	77	0.69	0.94	19	empty
5	101	0.68	0.91	23	empty

Interfaces

23 interfaces between chains.

B–C · 1761 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 1729 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 1687 Å² buried · 21 hydrogen bonds · protein-protein
E–H · 1641 Å² buried · 21 hydrogen bonds · protein-protein
E–G · 655 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3MM0 · Crystal structure of chimeric avidin · the same entry in another collection · chain K against K, 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 P02701
Every structure of UniProt P56734
Elsewhere: RCSB PDB 3MM0 · PDBe 3MM0 · UniProt P02701 · UniProt P56734

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