MolNFT v1 · #157159 · protein

Crystal structure of GTPase domain of human septin 12 in complex with gmppnp

6MQ9 · Septin-12: “Crystal structure of GTPase domain of human septin 12 in complex with gmppnp”. X-ray diffraction, 2 ligands (GNP, MG), 15 pockets (best druggability 0.77). MolNFT v1 #157159 on GenesisL1: 3D structure, binding sites and…

PDB: 6MQ9
Type: protein
Length: 1,057 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Septin-12
UniProt: Q8IYM1
Ligands: GNP, MG
Pockets: 15 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Septin-12	protein	265	42% helix, 22% strand	Q8IYM1
B	Septin-12	protein	267	40% helix, 21% strand	Q8IYM1
C	Septin-12	protein	264	40% helix, 21% strand	Q8IYM1
D	Septin-12	protein	261	39% helix, 22% strand	Q8IYM1

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, D, B, C
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

15 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	129	0.77	0.96	26	empty
2	469	0.68	0.80	61	GNP, MG
3	110	0.68	0.91	28	empty
4	263	0.64	0.82	43	GNP, MG
5	342	0.60	0.77	49	GNP, MG

Interfaces

6 interfaces between chains.

A–D · 1513 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 322 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 306 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 174 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 38 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6MQ9 · Crystal Structure of GTPase Domain of Human Septin 12 in complex with GMPPNP · the same entry in another collection · chain D against D, TM-score 1.00
Q8IYM1 · AlphaFold monomer V2.0 prediction for septin-12 (Q8IYM1) · a predicted model of the same protein · chain D 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 Q8IYM1
Elsewhere: RCSB PDB 6MQ9 · PDBe 6MQ9 · UniProt Q8IYM1

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