SMTL ID : 3cmb.1

Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: Y.163 Chain D: K.127, T.128, A.129 Ligands: PEG.9 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:T.128, D:A.129, A:Y.163, A:Y.163 Water bridges: A:Q.247, A:Q.247 NA.2: 5 residues within 4Å: Chain A: D.146, S.162, Y.163, E.164, G.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.146, A:S.162, A:G.165 Water bridges: A:E.164 NA.3: 6 residues within 4Å: Chain A: P.42, E.43, T.44, R.275, A.276, M.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.44 NA.11: 6 residues within 4Å: Chain A: L.150 Chain B: T.87, E.88, G.94, G.95, Q.96 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.88, B:G.94 NA.12: 4 residues within 4Å: Chain B: D.146, E.148 Chain D: E.164 Ligands: NA.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.148, D:E.164 Water bridges: B:I.147 NA.13: 6 residues within 4Å: Chain B: D.146, T.160, V.161, S.162 Chain D: G.165 Ligands: NA.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.146, B:E.148, B:S.162 NA.14: 5 residues within 4Å: Chain B: D.146, S.162, Y.163, E.164, G.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.162, B:G.165 NA.15: 4 residues within 4Å: Chain B: H.156, F.173, E.174 Ligands: PEG.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.156, B:F.173, B:F.173 Water bridges: B:F.157 NA.19: 5 residues within 4Å: Chain B: K.127, T.128, A.129 Chain C: Y.163 Ligands: CL.21 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.163, B:T.128, B:A.129 Water bridges: C:E.164 NA.20: 6 residues within 4Å: Chain C: P.42, E.43, T.44, R.275, A.276, M.277 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.42 NA.24: 6 residues within 4Å: Chain B: G.165 Chain D: D.146, I.147, T.160, V.161, S.162 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.148, D:T.160, D:S.162 NA.25: 6 residues within 4Å: Chain D: Y.163, F.168, L.239, S.244, Q.247, V.251 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.244, D:Q.247

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: E.164, N.166 Chain C: E.148, H.151, T.160 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain B: T.128, A.129 Chain C: I.143, Y.144, Q.247 Ligands: NA.19 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain D: R.275, G.278 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain A: T.128, A.129 Chain D: I.143, Y.144, Q.247 Ligand excluded by PLIP

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.5: 11 residues within 4Å: Chain A: V.46, N.84, W.91, L.99, N.101, Q.137, F.191, M.194, Y.218, Q.220, L.274 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.220 Water bridges: A:N.84, A:N.84, A:K.142, A:K.142 P33.16: 15 residues within 4Å: Chain B: A.52, S.54, A.82, N.84, W.91, Y.97, N.101, G.134, Q.137, F.191, M.194, T.196, Y.218, Q.220, L.274 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.54, B:Q.137, B:Q.220 Water bridges: B:N.84, B:N.84, B:K.142, B:K.142, B:K.142

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

PEG.6: 2 residues within 4Å: Chain A: H.156, D.172 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.173 PEG.7: 5 residues within 4Å: Chain A: E.238, L.239, T.240, P.241, N.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.238, A:N.252 PEG.8: 4 residues within 4Å: Chain A: W.199, S.213, F.215 Chain D: P.23 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.213, A:F.215 PEG.9: 7 residues within 4Å: Chain A: Y.144, Y.163, E.164 Chain D: K.127, T.128, Y.144 Ligands: NA.1 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:T.128, A:Y.163 Water bridges: D:T.128, A:T.128 PEG.10: 3 residues within 4Å: Chain A: Y.249 Chain D: F.35, G.37 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.248 PEG.17: 3 residues within 4Å: Chain B: H.156, D.172 Ligands: NA.15 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.233 PEG.18: 4 residues within 4Å: Chain B: W.199, S.213, F.215 Chain C: P.23 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.215 PEG.23: 3 residues within 4Å: Chain A: M.242 Chain C: V.153, H.156 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.156 PEG.29: 2 residues within 4Å: Chain D: H.156, D.172 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.172

2 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.22: 16 residues within 4Å: Chain C: T.44, V.46, A.52, S.54, N.84, W.91, Y.97, N.101, Q.137, F.191, M.194, Y.218, Q.220, L.274, A.276, M.277 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.54, C:S.54, C:Y.97, C:Q.220 Water bridges: C:Q.48, C:N.84, C:N.84, C:Q.137, C:Q.137, C:K.142, C:K.142, C:K.142, C:Y.218 PE8.28: 16 residues within 4Å: Chain D: V.46, S.54, A.82, N.84, W.91, Y.97, L.99, N.101, P.130, Q.137, F.191, M.194, Y.218, Q.220, L.274, A.276 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.54, D:S.54, D:Q.220 Water bridges: D:Q.48, D:N.84, D:N.84, D:K.142, D:K.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution. To be published

Release Date

2008-04-01

Peptides

Acetoacetate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acetoacetate decarboxylase