SMTL ID : 1e9y.1

CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE IN COMPLEX WITH ACETOHYDROXAMIC ACID

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-oligomer

Ligands

12 x HAE: ACETOHYDROXAMIC ACID(Non-covalent)

HAE.1: 11 residues within 4Å: Chain B: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.2, NI.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.274, B:A.365 HAE.4: 11 residues within 4Å: Chain D: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.5, NI.6 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.274, D:A.365 HAE.7: 11 residues within 4Å: Chain F: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.8, NI.9 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.274, F:A.365 HAE.10: 11 residues within 4Å: Chain H: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.11, NI.12 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:H.274, H:A.365 HAE.13: 11 residues within 4Å: Chain J: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.14, NI.15 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:H.274, J:A.365 HAE.16: 11 residues within 4Å: Chain L: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.17, NI.18 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:H.274, L:A.365 HAE.19: 11 residues within 4Å: Chain N: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.20, NI.21 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:H.274, N:A.365 HAE.22: 11 residues within 4Å: Chain P: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.23, NI.24 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:H.274, P:A.365 HAE.25: 11 residues within 4Å: Chain R: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.26, NI.27 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:H.274, R:A.365 HAE.28: 11 residues within 4Å: Chain T: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.29, NI.30 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:H.274, T:A.365 HAE.31: 11 residues within 4Å: Chain V: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.32, NI.33 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:H.274, V:A.365 HAE.34: 11 residues within 4Å: Chain X: H.136, A.169, K.219, H.221, H.248, H.274, G.279, D.362, A.365 Ligands: NI.35, NI.36 2 PLIP interactions: 2 interactions with chain X Hydrogen bonds: X:H.274, X:A.365

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

NI.2: 8 residues within 4Å: Chain B: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.1, NI.3 Ligand excluded by PLIP NI.3: 7 residues within 4Å: Chain B: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.1, NI.2 Ligand excluded by PLIP NI.5: 8 residues within 4Å: Chain D: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.4, NI.6 Ligand excluded by PLIP NI.6: 7 residues within 4Å: Chain D: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.4, NI.5 Ligand excluded by PLIP NI.8: 8 residues within 4Å: Chain F: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.7, NI.9 Ligand excluded by PLIP NI.9: 7 residues within 4Å: Chain F: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.7, NI.8 Ligand excluded by PLIP NI.11: 8 residues within 4Å: Chain H: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.10, NI.12 Ligand excluded by PLIP NI.12: 7 residues within 4Å: Chain H: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.10, NI.11 Ligand excluded by PLIP NI.14: 8 residues within 4Å: Chain J: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.13, NI.15 Ligand excluded by PLIP NI.15: 7 residues within 4Å: Chain J: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.13, NI.14 Ligand excluded by PLIP NI.17: 8 residues within 4Å: Chain L: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.16, NI.18 Ligand excluded by PLIP NI.18: 7 residues within 4Å: Chain L: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.16, NI.17 Ligand excluded by PLIP NI.20: 8 residues within 4Å: Chain N: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.19, NI.21 Ligand excluded by PLIP NI.21: 7 residues within 4Å: Chain N: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.19, NI.20 Ligand excluded by PLIP NI.23: 8 residues within 4Å: Chain P: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.22, NI.24 Ligand excluded by PLIP NI.24: 7 residues within 4Å: Chain P: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.22, NI.23 Ligand excluded by PLIP NI.26: 8 residues within 4Å: Chain R: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.25, NI.27 Ligand excluded by PLIP NI.27: 7 residues within 4Å: Chain R: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.25, NI.26 Ligand excluded by PLIP NI.29: 8 residues within 4Å: Chain T: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.28, NI.30 Ligand excluded by PLIP NI.30: 7 residues within 4Å: Chain T: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.28, NI.29 Ligand excluded by PLIP NI.32: 8 residues within 4Å: Chain V: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.31, NI.33 Ligand excluded by PLIP NI.33: 7 residues within 4Å: Chain V: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.31, NI.32 Ligand excluded by PLIP NI.35: 8 residues within 4Å: Chain X: H.136, K.219, H.221, H.248, H.274, G.279 Ligands: HAE.34, NI.36 Ligand excluded by PLIP NI.36: 7 residues within 4Å: Chain X: H.136, H.138, T.171, K.219, D.362 Ligands: HAE.34, NI.35 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ha, N.-C. et al., Supramolecular Assembly and Acid Resistance of Helicobacter Pylori Urease. Nat.Struct.Biol. (2001)

Release Date

2001-11-01

Peptides

UREASE SUBUNIT ALPHA: ACEGIKMOQSUW
UREASE SUBUNIT BETA: BDFHJLNPRTVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

M
A

O
A

Q
A

S
A

U
A

W
A

B
B

D
B

F
B

H
B

J
B

L
B

N
B

P
B

R
B

T
B

V
B

X
B

UREASE SUBUNIT ALPHA

UREASE SUBUNIT BETA

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