SMTL ID : 7kns.1

Cryo-EM structure of jack bean urease

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: K.490, H.492, H.519, H.545 Ligands: PO4.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.519, A:H.545 NI.3: 5 residues within 4Å: Chain B: K.490, H.492, H.519, H.545 Ligands: PO4.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.519, B:H.545 NI.5: 8 residues within 4Å: Chain C: H.407, H.409, K.490, H.492, H.519, H.545, D.633 Ligands: PO4.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.407 NI.7: 6 residues within 4Å: Chain D: H.407, K.490, H.492, H.519, H.545 Ligands: PO4.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.519, D:H.545 NI.9: 5 residues within 4Å: Chain E: K.490, H.492, H.519, H.545 Ligands: PO4.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.519, E:H.545 NI.11: 5 residues within 4Å: Chain F: K.490, H.492, H.519, H.545 Ligands: PO4.12 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.519, F:H.545

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 10 residues within 4Å: Chain A: A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636, M.637 Ligands: NI.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.550 Salt bridges: A:H.492, A:H.519 PO4.4: 11 residues within 4Å: Chain B: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636 Ligands: NI.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.636 Salt bridges: B:H.407, B:H.409, B:H.492, B:H.519, B:H.545 PO4.6: 11 residues within 4Å: Chain C: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636 Ligands: NI.5 5 PLIP interactions: 5 interactions with chain C Salt bridges: C:H.407, C:H.409, C:H.492, C:H.519, C:H.545 PO4.8: 11 residues within 4Å: Chain D: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636 Ligands: NI.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:A.440, D:G.550 Salt bridges: D:H.407, D:H.409, D:H.492, D:H.519, D:H.545 PO4.10: 11 residues within 4Å: Chain E: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636 Ligands: NI.9 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:D.633 Salt bridges: E:H.407, E:H.409, E:H.492, E:H.519, E:H.545 PO4.12: 9 residues within 4Å: Chain F: A.440, K.490, H.492, H.519, G.550, D.633, A.636, M.637 Ligands: NI.11 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:A.440, F:G.550 Salt bridges: F:H.492, F:H.519

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feathers, J.R. et al., Experimental evaluation of super-resolution imaging and magnification choice in single-particle cryo-EM. J Struct Biol X (2021)

Release Date

2021-03-24

Peptides

Urease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Urease

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