MolNFT v1 · #150602 · protein + DNA

Structure of a yeast closed complex with distorted DNA (ccdist)

6GYM: “Structure of a yeast closed complex with distorted DNA (ccdist)”. Electron microscopy, 3 ligands (SF4, ZN, MG). MolNFT v1 #150602 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GYM
Type: protein + DNA
Length: 8,338 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145
Ligands: SF4, ZN, MG

Structure

electron microscopy · 31 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	—	protein	698	—	P06839
1	—	protein	491	—	P32776
2	—	protein	395	—	Q02939
3	—	protein	138	—	Q03290
4	—	protein	297	—	Q12004
5	—	protein	66	—	Q3E7C1
6	—	protein	335	—	Q04673
7	—	protein	408	—	Q00578
A	—	protein	1398	—	P04050
B	—	protein	1152	—	P08518
C	—	protein	262	—	P16370
D	—	protein	157	—	P20433
E	—	protein	213	—	P20434
F	—	protein	83	—	P20435
G	—	protein	171	—	P34087
H	—	protein	136	—	P20436
I	—	protein	116	—	P27999
J	—	protein	65	—	P22139
K	—	protein	112	—	P38902
L	—	protein	45	—	P40422
M	—	protein	279	—	P29055
O	—	protein	180	—	P13393
Q	—	protein	148	—	P41895
R	—	protein	190	—	P41896
U	—	protein	92	—	P32773
V	—	protein	100	—	P32774
W	—	protein	258	—	P36100
X	—	protein	160	—	P36145
Z	—	protein	43	—	—
N	—	dna	75	—	—
T	—	dna	75	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains 0
ZN · Zinc ion · metal · 16 copies · chains 3, W, 4, 6, A, B, C, I, J, L, M
MG · Magnesium ion · metal · chains A

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

Compared structures

6GYM · Structure of a yeast closed complex with distorted DNA (CCdist) · the same entry in another collection · chain B against B, 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 P06839
Every structure of UniProt P32776
Every structure of UniProt Q02939
Every structure of UniProt Q03290
Every structure of UniProt Q12004
Every structure of UniProt Q3E7C1
Every structure of UniProt Q04673
Every structure of UniProt Q00578
Every structure of UniProt P04050
Every structure of UniProt P08518
Every structure of UniProt P16370
Every structure of UniProt P20433
Every structure of UniProt P20434
Every structure of UniProt P20435
Every structure of UniProt P34087
Every structure of UniProt P20436
Every structure of UniProt P27999
Every structure of UniProt P22139
Every structure of UniProt P38902
Every structure of UniProt P40422
Every structure of UniProt P29055
Every structure of UniProt P13393
Every structure of UniProt P41895
Every structure of UniProt P41896
Every structure of UniProt P32773
Every structure of UniProt P32774
Every structure of UniProt P36100
Every structure of UniProt P36145
Elsewhere: RCSB PDB 6GYM · PDBe 6GYM · UniProt P06839 · UniProt P32776 · UniProt Q02939 · UniProt Q03290 · UniProt Q12004 · UniProt Q3E7C1 · UniProt Q04673 · UniProt Q00578 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P29055 · UniProt P13393 · UniProt P41895 · UniProt P41896 · UniProt P32773 · UniProt P32774 · UniProt P36100 · UniProt P36145

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