SMTL ID : 6qsu.1

Helicobacter pylori urease with BME bound in the active site

Coordinates

PDB Format Compare

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, BME.3 Ligand excluded by PLIP NI.2: 7 residues within 4Å: Chain B: H.136, H.138, T.171, K.219, D.362 Ligands: NI.1, BME.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, BME.6 Ligand excluded by PLIP NI.5: 7 residues within 4Å: Chain N: H.136, H.138, T.171, K.219, D.362 Ligands: NI.4, BME.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, BME.9 Ligand excluded by PLIP NI.8: 7 residues within 4Å: Chain O: H.136, H.138, T.171, K.219, D.362 Ligands: NI.7, BME.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, BME.12 Ligand excluded by PLIP NI.11: 7 residues within 4Å: Chain P: H.136, H.138, T.171, K.219, D.362 Ligands: NI.10, BME.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, BME.15 Ligand excluded by PLIP NI.14: 7 residues within 4Å: Chain Q: H.136, H.138, T.171, K.219, D.362 Ligands: NI.13, BME.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, BME.18 Ligand excluded by PLIP NI.17: 7 residues within 4Å: Chain R: H.136, H.138, T.171, K.219, D.362 Ligands: NI.16, BME.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, BME.21 Ligand excluded by PLIP NI.20: 7 residues within 4Å: Chain S: H.136, H.138, T.171, K.219, D.362 Ligands: NI.19, BME.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, BME.24 Ligand excluded by PLIP NI.23: 7 residues within 4Å: Chain T: H.136, H.138, T.171, K.219, D.362 Ligands: NI.22, BME.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, BME.27 Ligand excluded by PLIP NI.26: 7 residues within 4Å: Chain U: H.136, H.138, T.171, K.219, D.362 Ligands: NI.25, BME.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, BME.30 Ligand excluded by PLIP NI.29: 7 residues within 4Å: Chain V: H.136, H.138, T.171, K.219, D.362 Ligands: NI.28, BME.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, BME.33 Ligand excluded by PLIP NI.32: 7 residues within 4Å: Chain W: H.136, H.138, T.171, K.219, D.362 Ligands: NI.31, BME.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, BME.36 Ligand excluded by PLIP NI.35: 7 residues within 4Å: Chain X: H.136, H.138, T.171, K.219, D.362 Ligands: NI.34, BME.36 Ligand excluded by PLIP

12 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 12 residues within 4Å: Chain B: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.1, NI.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.279 BME.6: 12 residues within 4Å: Chain N: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.4, NI.5 No protein-ligand interaction detected (PLIP) BME.9: 12 residues within 4Å: Chain O: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.7, NI.8 No protein-ligand interaction detected (PLIP) BME.12: 12 residues within 4Å: Chain P: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.10, NI.11 No protein-ligand interaction detected (PLIP) BME.15: 12 residues within 4Å: Chain Q: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.13, NI.14 No protein-ligand interaction detected (PLIP) BME.18: 12 residues within 4Å: Chain R: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.16, NI.17 No protein-ligand interaction detected (PLIP) BME.21: 12 residues within 4Å: Chain S: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.19, NI.20 No protein-ligand interaction detected (PLIP) BME.24: 12 residues within 4Å: Chain T: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.22, NI.23 No protein-ligand interaction detected (PLIP) BME.27: 12 residues within 4Å: Chain U: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.25, NI.26 No protein-ligand interaction detected (PLIP) BME.30: 12 residues within 4Å: Chain V: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.28, NI.29 No protein-ligand interaction detected (PLIP) BME.33: 12 residues within 4Å: Chain W: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.31, NI.32 No protein-ligand interaction detected (PLIP) BME.36: 12 residues within 4Å: Chain X: H.138, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365, M.366 Ligands: NI.34, NI.35 No protein-ligand interaction detected (PLIP)

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

2021-01-20

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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