SMTL ID : 5g3p.1

Bacillus cereus formamidase (BceAmiF) acetylated at the active site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-hexamer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: N.293, P.294, T.296 Chain B: G.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.146, B:G.148 PEG.2: 5 residues within 4Å: Chain A: T.68, K.69, Y.322, G.323, Y.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.69, A:G.323 PEG.7: 11 residues within 4Å: Chain B: V.243, Q.244, G.245, E.251, I.252, V.253 Chain E: T.193, S.196, E.197, R.247 Ligands: NA.14 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:S.196, E:E.197, E:E.197, E:R.247, E:R.247, B:Q.244, B:I.252 Water bridges: E:S.196 PEG.8: 6 residues within 4Å: Chain B: T.68, K.69, Y.322, Y.324 Chain C: S.48, G.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.68, B:T.68, B:K.69 PEG.23: 5 residues within 4Å: Chain A: W.250 Chain D: V.25, Y.222, D.223, G.224 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.38, A:Q.38 PEG.24: 5 residues within 4Å: Chain C: G.148 Chain D: N.293, P.294, T.296, K.299 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.146 PEG.25: 10 residues within 4Å: Chain D: V.243, Q.244, G.245, E.251, I.252, V.253 Chain F: T.193, S.196, E.197, R.247 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:Q.244, F:R.247 Water bridges: F:R.247 PEG.27: 5 residues within 4Å: Chain E: T.68, K.69, Y.322, G.323, Y.324 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:T.68, E:K.69 Water bridges: E:T.68, B:S.48 PEG.28: 4 residues within 4Å: Chain E: P.81, G.82, P.83, D.86 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.86 PEG.34: 7 residues within 4Å: Chain E: D.146, G.148 Chain F: N.293, P.294, T.296, K.299 Ligands: NA.33 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Water bridges: F:N.293 Hydrogen bonds: E:D.146 PEG.35: 11 residues within 4Å: Chain A: T.193, S.196, E.197, R.247 Chain F: V.243, Q.244, G.245, E.251, I.252, V.253 Ligands: NA.42 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:S.196, A:R.247, A:R.247, F:Q.244, F:E.251, F:E.251 Water bridges: A:S.196 PEG.36: 4 residues within 4Å: Chain F: V.25, Y.222, D.223, G.224 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.250 Water bridges: D:K.41

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: M.200, Q.233, T.241, Q.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.241, A:Q.244 EDO.19: 4 residues within 4Å: Chain C: Y.222, G.224 Chain E: Q.38, W.250 1 PLIP interactions: 1 interactions with chain E Water bridges: E:W.250 EDO.30: 5 residues within 4Å: Chain E: M.200, R.204, Q.233, T.241, Q.244 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.233, E:Q.244 Water bridges: E:R.204

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: P.309, W.310, E.311, D.312, E.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.312, A:D.312 Water bridges: A:E.311 ACT.12: 3 residues within 4Å: Chain B: P.81, G.82, D.86 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.81 ACT.20: 4 residues within 4Å: Chain C: P.81, G.82, P.83, D.86 No protein-ligand interaction detected (PLIP) ACT.39: 6 residues within 4Å: Chain F: P.309, W.310, E.311, D.312, E.313 Ligands: NA.40 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.312, F:D.312, F:D.312

15 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: N.293, K.299 Chain B: A.302 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.293, B:A.302 Water bridges: A:N.293, A:N.293 NA.6: 1 residues within 4Å: Chain B: G.304 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.292 NA.13: 4 residues within 4Å: Chain B: S.4, G.5 Chain E: Q.194, Q.198 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.198 NA.14: 7 residues within 4Å: Chain B: V.243, I.252, V.253, T.254 Chain E: T.193, Q.194 Ligands: PEG.7 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:T.193, E:T.193, B:T.254 Water bridges: B:T.254 NA.15: 4 residues within 4Å: Chain B: T.79, V.80, E.105, K.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.80, B:E.105, B:E.105 NA.16: 3 residues within 4Å: Chain B: T.73, E.75, F.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.75, B:E.75 Water bridges: B:K.70, B:E.75 NA.21: 4 residues within 4Å: Chain B: Q.194, Q.198 Chain C: S.4, G.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.5 NA.22: 5 residues within 4Å: Chain C: P.171, S.205, N.206, Q.209 Chain D: Q.209 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.205, C:Q.209, D:Q.209 Water bridges: C:N.206 NA.31: 6 residues within 4Å: Chain E: P.171, E.172, R.175 Chain F: P.171, E.172, F.297 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.172 NA.32: 4 residues within 4Å: Chain E: S.12, G.156, P.259, E.260 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.260, E:E.260, E:E.260 NA.33: 1 residues within 4Å: Ligands: PEG.34 2 PLIP interactions: 2 interactions with chain E Water bridges: E:G.145, E:D.146 NA.40: 4 residues within 4Å: Chain F: K.307, V.308, P.309 Ligands: ACT.39 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:P.309, F:E.311 NA.41: 2 residues within 4Å: Chain F: H.44, S.48 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.44 NA.42: 7 residues within 4Å: Chain A: T.193, Q.194 Chain F: V.243, I.252, V.253, T.254 Ligands: PEG.35 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:T.254, F:T.254 Water bridges: A:S.196 NA.43: 4 residues within 4Å: Chain E: N.134, F.170 Chain F: N.277, R.281 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.277

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 4 residues within 4Å: Chain B: V.80, P.81, M.126, K.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.129 Water bridges: B:V.80 PGE.17: 6 residues within 4Å: Chain C: T.68, K.69, Y.322, G.323, Y.324 Chain E: S.48 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.68, C:K.69, C:G.323 Water bridges: C:T.68 PGE.18: 5 residues within 4Å: Chain C: N.293, P.294, T.296, K.299 Chain D: G.148 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:K.299, D:D.146 PGE.26: 6 residues within 4Å: Chain A: S.48 Chain D: T.68, K.69, Y.322, G.323, Y.324 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.68, D:K.69, D:G.323 Water bridges: D:T.68 PGE.29: 6 residues within 4Å: Chain E: N.293, P.294, Y.295, T.296, K.299 Chain F: D.146 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Water bridges: E:N.293, F:G.148 Hydrogen bonds: F:D.146 PGE.37: 6 residues within 4Å: Chain D: S.48 Chain F: T.68, K.69, Y.322, G.323, Y.324 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:T.68, F:K.69 Water bridges: F:T.68, D:S.48, D:S.48

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

PG4.10: 6 residues within 4Å: Chain A: D.146, G.148 Chain B: N.293, P.294, T.296, K.299 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.299

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

PO4.11: 9 residues within 4Å: Chain B: H.246, R.247, N.248 Chain C: H.246, R.247, N.248 Chain E: H.246, R.247, N.248 9 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, 3 interactions with chain E Hydrogen bonds: C:R.247, C:N.248, B:R.247, B:N.248, E:R.247, E:N.248 Salt bridges: C:H.246, B:H.246, E:H.246 PO4.38: 9 residues within 4Å: Chain A: H.246, R.247, N.248 Chain D: H.246, R.247, N.248 Chain F: H.246, R.247, N.248 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D, 3 interactions with chain F Hydrogen bonds: A:R.247, A:N.248, D:R.247, D:N.248, F:R.247, F:N.248 Salt bridges: A:H.246, D:H.246, F:H.246

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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