SMTL ID : 6yl3.1

High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-12-mer

Ligands

24 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 8 residues within 4Å: Chain C: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.2 Ligand excluded by PLIP NI.2: 7 residues within 4Å: Chain C: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.1 Ligand excluded by PLIP NI.3: 8 residues within 4Å: Chain F: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.4 Ligand excluded by PLIP NI.4: 7 residues within 4Å: Chain F: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.3 Ligand excluded by PLIP NI.5: 8 residues within 4Å: Chain I: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.6 Ligand excluded by PLIP NI.6: 7 residues within 4Å: Chain I: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.5 Ligand excluded by PLIP NI.7: 8 residues within 4Å: Chain L: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.8 Ligand excluded by PLIP NI.8: 7 residues within 4Å: Chain L: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.7 Ligand excluded by PLIP NI.9: 8 residues within 4Å: Chain O: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.10 Ligand excluded by PLIP NI.10: 7 residues within 4Å: Chain O: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.9 Ligand excluded by PLIP NI.11: 8 residues within 4Å: Chain R: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.12 Ligand excluded by PLIP NI.12: 7 residues within 4Å: Chain R: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.11 Ligand excluded by PLIP NI.13: 8 residues within 4Å: Chain U: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.14 Ligand excluded by PLIP NI.14: 7 residues within 4Å: Chain U: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.13 Ligand excluded by PLIP NI.15: 8 residues within 4Å: Chain X: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.16 Ligand excluded by PLIP NI.16: 7 residues within 4Å: Chain X: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.15 Ligand excluded by PLIP NI.17: 8 residues within 4Å: Chain 0: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.18 Ligand excluded by PLIP NI.18: 7 residues within 4Å: Chain 0: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.17 Ligand excluded by PLIP NI.19: 8 residues within 4Å: Chain 3: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.20 Ligand excluded by PLIP NI.20: 7 residues within 4Å: Chain 3: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.19 Ligand excluded by PLIP NI.21: 8 residues within 4Å: Chain 6: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.22 Ligand excluded by PLIP NI.22: 7 residues within 4Å: Chain 6: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.21 Ligand excluded by PLIP NI.23: 8 residues within 4Å: Chain 9: H.138, K.221, H.223, H.250, F.275, H.276, G.281 Ligands: NI.24 Ligand excluded by PLIP NI.24: 7 residues within 4Å: Chain 9: H.138, H.140, T.173, K.221, D.364, A.367 Ligands: NI.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Righetto, R.D. et al., High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. Nat Commun (2020)

Release Date

2020-05-06

Peptides

Urease subunit gamma: ADGJMPSVY147
Urease subunit beta: BEHKNQTWZ258
Urease subunit alpha: CFILORUX0369

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
J

M
M

P
P

S
S

V
W

Y
Z

1
2

4
5

7
8

B
B

E
E

H
H

K
K

N
N

Q
Q

T
T

W
X

Z
0

2
3

5
6

8
9

C
C

F
F

I
I

L
L

O
O

R
R

U
V

X
Y

0
1

3
4

6
7

9
U

Urease subunit gamma

Urease subunit beta

Urease subunit alpha

Related Entries With Identical Sequence