MolNFT v1 · #156537 · protein

Structure of REV7-R124A complexed with SHLD3(37-73)

6M7B · Mitotic spindle assembly checkpoint protein MAD2B: “Structure of REV7-R124A complexed with SHLD3(37-73)”. X-ray diffraction, 5 pockets (best druggability 0.82). MolNFT v1 #156537 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6M7B
Type: protein
Length: 473 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitotic spindle assembly checkpoint protein MAD2B; Shieldin complex subunit 3
UniProt: Q9UI95, Q6ZNX1
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitotic spindle assembly checkpoint protein MAD2B	protein	201	38% helix, 30% strand	Q9UI95
B	Mitotic spindle assembly checkpoint protein MAD2B	protein	200	38% helix, 30% strand	Q9UI95
C, D	Shieldin complex subunit 3	protein	36	28% helix, 8% strand	Q6ZNX1

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	965	0.82	0.83	70	empty
2	200	0.57	0.80	24	empty
3	166	0.52	0.78	23	empty
4	66	0.48	0.84	23	empty
5	53	0.31	0.77	15	empty

Interfaces

5 interfaces between chains.

B–C · 1888 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 1820 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 721 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 370 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 298 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6M7B · Structure of REV7-R124A complexed with SHLD3(37-73) · the same entry in another collection · chain A against A, TM-score 1.00
Q9UI95 · AlphaFold monomer V2.0 prediction for mitotic spindle assembly checkpoint protein MAD2B… · a predicted model of the same protein · chain B against A, TM-score 0.98
Q6ZNX1 · AlphaFold monomer V2.0 prediction for shieldin complex subunit 3 (Q6ZNX1) · a predicted model of the same protein · chain C against A, TM-score 0.57

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 Q9UI95
Every structure of UniProt Q6ZNX1
Elsewhere: RCSB PDB 6M7B · PDBe 6M7B · UniProt Q9UI95 · UniProt Q6ZNX1

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