SMTL ID : 5g3o.1

Bacillus cereus formamidase (BceAmiF) inhibited with urea.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

23 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 6 residues within 4Å: Chain A: E.197 Chain C: T.241, L.242, Q.244 Chain F: R.204, T.240 Ligand excluded by PLIP PEG.2: 4 residues within 4Å: Chain A: N.293, P.294, K.299 Chain F: G.148 Ligand excluded by PLIP PEG.3: 4 residues within 4Å: Chain A: V.151, D.153, K.159, K.180 Ligand excluded by PLIP PEG.6: 4 residues within 4Å: Chain B: E.197 Chain F: T.241, L.242, Q.244 Ligand excluded by PLIP PEG.7: 5 residues within 4Å: Chain B: N.293, P.294, T.296, K.299 Chain C: G.148 Ligand excluded by PLIP PEG.8: 4 residues within 4Å: Chain B: V.151, D.153, K.159, K.180 Ligand excluded by PLIP PEG.9: 1 residues within 4Å: Chain B: M.126 Ligand excluded by PLIP PEG.11: 5 residues within 4Å: Chain C: V.151, C.152, D.153, K.159, K.180 Ligand excluded by PLIP PEG.12: 4 residues within 4Å: Chain B: G.148 Chain C: N.293, P.294, K.299 Ligand excluded by PLIP PEG.13: 5 residues within 4Å: Chain B: T.240 Chain C: E.197 Chain D: T.241, L.242, Q.244 Ligand excluded by PLIP PEG.16: 5 residues within 4Å: Chain D: N.293, P.294, T.296, K.299 Chain E: G.148 Ligand excluded by PLIP PEG.17: 4 residues within 4Å: Chain D: V.151, D.153, K.159, K.180 Ligand excluded by PLIP PEG.18: 3 residues within 4Å: Chain A: T.241, L.242 Chain D: E.197 Ligand excluded by PLIP PEG.19: 4 residues within 4Å: Chain C: Y.222, G.224 Chain D: K.41, W.250 Ligand excluded by PLIP PEG.20: 4 residues within 4Å: Chain B: T.241, L.242, Q.244 Chain E: E.197 Ligand excluded by PLIP PEG.21: 3 residues within 4Å: Chain E: M.126, I.127, K.129 Ligand excluded by PLIP PEG.22: 5 residues within 4Å: Chain E: Q.38, W.250 Chain F: Y.222, D.223, G.224 Ligand excluded by PLIP PEG.23: 4 residues within 4Å: Chain E: V.151, D.153, K.159, K.180 Ligand excluded by PLIP PEG.24: 3 residues within 4Å: Chain E: N.293, P.294, K.299 Ligand excluded by PLIP PEG.25: 4 residues within 4Å: Chain A: T.240 Chain E: T.241, L.242 Chain F: E.197 Ligand excluded by PLIP PEG.26: 4 residues within 4Å: Chain F: V.151, D.153, K.159, K.180 Ligand excluded by PLIP PEG.27: 4 residues within 4Å: Chain B: T.68, K.69 Chain F: S.48 Ligands: P4G.29 Ligand excluded by PLIP PEG.28: 6 residues within 4Å: Chain A: D.146, G.148 Chain F: N.293, P.294, T.296, K.299 Ligand excluded by PLIP

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 5 residues within 4Å: Chain A: K.41, W.250 Chain D: V.25, D.223, G.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.41 PG4.5: 7 residues within 4Å: Chain A: V.25, Y.222, D.223, G.224 Chain C: Q.38, K.41, W.250 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.38, C:K.41

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

PO4.10: 9 residues within 4Å: Chain B: H.246, R.247, N.248 Chain E: H.246, R.247, N.248 Chain F: H.246, R.247, N.248 9 PLIP interactions: 3 interactions with chain F, 3 interactions with chain B, 3 interactions with chain E Hydrogen bonds: F:R.247, F:N.248, B:R.247, B:N.248, E:R.247, E:N.248 Salt bridges: F:H.246, B:H.246, E:H.246 PO4.15: 9 residues within 4Å: Chain A: H.246, R.247, N.248 Chain C: H.246, R.247, N.248 Chain D: H.246, R.247, N.248 9 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: C:R.247, C:N.248, D:R.247, D:N.248, A:R.247, A:N.248 Salt bridges: C:H.246, D:H.246, A:H.246

2 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.14: 9 residues within 4Å: Chain C: N.236, F.237, D.238, Y.258 Chain F: F.237, A.255, E.256, Y.258, L.261 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:F.237, F:A.255, C:Y.258 Hydrogen bonds: C:N.236 P4G.29: 7 residues within 4Å: Chain B: Y.222, D.223, G.224 Chain F: Q.38, K.41, W.250 Ligands: PEG.27 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.250 Hydrogen bonds: F:K.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Rodriguez, S. et al., A novel cysteine carbamoyl-switch is responsible for the inhibition of formamidase, a nitrilase superfamily member. Arch.Biochem.Biophys. (2019)

Release Date

2017-04-12

Peptides

FORMAMIDASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

FORMAMIDASE

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