SMTL ID : 6zja.1

Helicobacter pylori urease with inhibitor bound in the active site

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-mer

Ligands

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

NI.1: 7 residues within 4Å: Chain B: K.219, H.221, H.248, H.274, G.279 Ligands: NI.2, DJM.3 Ligand excluded by PLIP NI.2: 6 residues within 4Å: Chain B: H.136, H.138, K.219, D.362 Ligands: NI.1, DJM.3 Ligand excluded by PLIP NI.4: 7 residues within 4Å: Chain N: K.219, H.221, H.248, H.274, G.279 Ligands: NI.5, DJM.6 Ligand excluded by PLIP NI.5: 6 residues within 4Å: Chain N: H.136, H.138, K.219, D.362 Ligands: NI.4, DJM.6 Ligand excluded by PLIP NI.7: 7 residues within 4Å: Chain O: K.219, H.221, H.248, H.274, G.279 Ligands: NI.8, DJM.9 Ligand excluded by PLIP NI.8: 6 residues within 4Å: Chain O: H.136, H.138, K.219, D.362 Ligands: NI.7, DJM.9 Ligand excluded by PLIP NI.10: 7 residues within 4Å: Chain P: K.219, H.221, H.248, H.274, G.279 Ligands: NI.11, DJM.12 Ligand excluded by PLIP NI.11: 6 residues within 4Å: Chain P: H.136, H.138, K.219, D.362 Ligands: NI.10, DJM.12 Ligand excluded by PLIP NI.13: 7 residues within 4Å: Chain Q: K.219, H.221, H.248, H.274, G.279 Ligands: NI.14, DJM.15 Ligand excluded by PLIP NI.14: 6 residues within 4Å: Chain Q: H.136, H.138, K.219, D.362 Ligands: NI.13, DJM.15 Ligand excluded by PLIP NI.16: 7 residues within 4Å: Chain R: K.219, H.221, H.248, H.274, G.279 Ligands: NI.17, DJM.18 Ligand excluded by PLIP NI.17: 6 residues within 4Å: Chain R: H.136, H.138, K.219, D.362 Ligands: NI.16, DJM.18 Ligand excluded by PLIP NI.19: 7 residues within 4Å: Chain S: K.219, H.221, H.248, H.274, G.279 Ligands: NI.20, DJM.21 Ligand excluded by PLIP NI.20: 6 residues within 4Å: Chain S: H.136, H.138, K.219, D.362 Ligands: NI.19, DJM.21 Ligand excluded by PLIP NI.22: 7 residues within 4Å: Chain T: K.219, H.221, H.248, H.274, G.279 Ligands: NI.23, DJM.24 Ligand excluded by PLIP NI.23: 6 residues within 4Å: Chain T: H.136, H.138, K.219, D.362 Ligands: NI.22, DJM.24 Ligand excluded by PLIP NI.25: 7 residues within 4Å: Chain U: K.219, H.221, H.248, H.274, G.279 Ligands: NI.26, DJM.27 Ligand excluded by PLIP NI.26: 6 residues within 4Å: Chain U: H.136, H.138, K.219, D.362 Ligands: NI.25, DJM.27 Ligand excluded by PLIP NI.28: 7 residues within 4Å: Chain V: K.219, H.221, H.248, H.274, G.279 Ligands: NI.29, DJM.30 Ligand excluded by PLIP NI.29: 6 residues within 4Å: Chain V: H.136, H.138, K.219, D.362 Ligands: NI.28, DJM.30 Ligand excluded by PLIP NI.31: 7 residues within 4Å: Chain W: K.219, H.221, H.248, H.274, G.279 Ligands: NI.32, DJM.33 Ligand excluded by PLIP NI.32: 6 residues within 4Å: Chain W: H.136, H.138, K.219, D.362 Ligands: NI.31, DJM.33 Ligand excluded by PLIP NI.34: 7 residues within 4Å: Chain X: K.219, H.221, H.248, H.274, G.279 Ligands: NI.35, DJM.36 Ligand excluded by PLIP NI.35: 6 residues within 4Å: Chain X: H.136, H.138, K.219, D.362 Ligands: NI.34, DJM.36 Ligand excluded by PLIP

12 x DJM: 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide(Non-covalent)

DJM.3: 17 residues within 4Å: Chain B: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Chain U: I.467 Ligands: NI.1, NI.2 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain U Hydrophobic interactions: B:L.318, B:M.366, U:I.467 Hydrogen bonds: B:H.221, B:D.362 pi-Stacking: B:H.322 DJM.6: 17 residues within 4Å: Chain N: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Chain R: I.467 Ligands: NI.4, NI.5 7 PLIP interactions: 6 interactions with chain N, 1 interactions with chain R Hydrophobic interactions: N:L.318, N:M.366, R:I.467 Hydrogen bonds: N:H.221, N:H.248, N:D.362 pi-Stacking: N:H.322 DJM.9: 17 residues within 4Å: Chain O: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Chain X: I.467 Ligands: NI.7, NI.8 6 PLIP interactions: 5 interactions with chain O, 1 interactions with chain X Hydrophobic interactions: O:L.318, O:M.366, X:I.467 Hydrogen bonds: O:H.221, O:D.362 pi-Stacking: O:H.322 DJM.12: 17 residues within 4Å: Chain P: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Chain W: I.467 Ligands: NI.10, NI.11 6 PLIP interactions: 5 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:L.318, P:M.366, W:I.467 Hydrogen bonds: P:H.221, P:D.362 pi-Stacking: P:H.322 DJM.15: 17 residues within 4Å: Chain O: I.467 Chain Q: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Ligands: NI.13, NI.14 6 PLIP interactions: 5 interactions with chain Q, 1 interactions with chain O Hydrophobic interactions: Q:L.318, Q:M.366, O:I.467 Hydrogen bonds: Q:H.221, Q:D.362 pi-Stacking: Q:H.322 DJM.18: 17 residues within 4Å: Chain R: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Chain V: I.467 Ligands: NI.16, NI.17 7 PLIP interactions: 6 interactions with chain R, 1 interactions with chain V Hydrophobic interactions: R:L.318, R:M.366, V:I.467 Hydrogen bonds: R:H.221, R:H.248, R:D.362 pi-Stacking: R:H.322 DJM.21: 17 residues within 4Å: Chain B: I.467 Chain S: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Ligands: NI.19, NI.20 7 PLIP interactions: 6 interactions with chain S, 1 interactions with chain B Hydrophobic interactions: S:L.318, S:M.366, B:I.467 Hydrogen bonds: S:H.221, S:H.248, S:D.362 pi-Stacking: S:H.322 DJM.24: 17 residues within 4Å: Chain P: I.467 Chain T: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Ligands: NI.22, NI.23 7 PLIP interactions: 6 interactions with chain T, 1 interactions with chain P Hydrophobic interactions: T:L.318, T:M.366, P:I.467 Hydrogen bonds: T:H.221, T:H.248, T:D.362 pi-Stacking: T:H.322 DJM.27: 17 residues within 4Å: Chain S: I.467 Chain U: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Ligands: NI.25, NI.26 6 PLIP interactions: 5 interactions with chain U, 1 interactions with chain S Hydrophobic interactions: U:L.318, U:M.366, S:I.467 Hydrogen bonds: U:H.221, U:D.362 pi-Stacking: U:H.322 DJM.30: 17 residues within 4Å: Chain N: I.467 Chain V: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Ligands: NI.28, NI.29 7 PLIP interactions: 6 interactions with chain V, 1 interactions with chain N Hydrophobic interactions: V:L.318, V:M.366, N:I.467 Hydrogen bonds: V:H.221, V:H.248, V:D.362 pi-Stacking: V:H.322 DJM.33: 17 residues within 4Å: Chain T: I.467 Chain W: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Ligands: NI.31, NI.32 6 PLIP interactions: 5 interactions with chain W, 1 interactions with chain T Hydrophobic interactions: W:L.318, W:M.366, T:I.467 Hydrogen bonds: W:H.221, W:D.362 pi-Stacking: W:H.322 DJM.36: 17 residues within 4Å: Chain Q: I.467 Chain X: A.169, K.219, H.221, H.248, H.274, A.278, G.279, M.317, L.318, C.321, H.322, D.362, A.365, M.366 Ligands: NI.34, NI.35 7 PLIP interactions: 6 interactions with chain X, 1 interactions with chain Q Hydrophobic interactions: X:L.318, X:M.366, Q:I.467 Hydrogen bonds: X:H.221, X:H.248, X:D.362 pi-Stacking: X:H.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cunha, E.S. et al., Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 angstrom resolution. Nat Commun (2021)

Release Date

2020-12-23

Peptides

Urease subunit alpha: ACDEFGHIJKLM
Urease subunit beta: BNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
E

E
G

F
I

G
K

H
M

I
O

J
Q

K
S

L
U

M
W

B
B

N
J

O
D

P
F

Q
H

R
L

S
N

T
P

U
R

V
T

W
V

X
X

Urease subunit alpha

Urease subunit beta

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