SMTL ID : 1saz.1

Membership in the ASKHA Superfamily: Enzymological Properties and Crystal Structure of Butyrate Kinase 2 from Thermotoga maritima

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-octamer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: F.210, S.215, G.216, T.217 Chain F: S.142, G.143 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.142 NA.7: 6 residues within 4Å: Chain B: F.210, S.215, G.216, T.217 Chain E: S.142, G.143 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.280 NA.13: 6 residues within 4Å: Chain C: F.210, S.215, G.216, T.217 Chain G: S.142, G.143 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.216 NA.19: 6 residues within 4Å: Chain D: F.210, S.215, G.216, T.217 Chain H: S.142, G.143 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.217 NA.25: 6 residues within 4Å: Chain B: S.142, G.143 Chain E: F.210, S.215, G.216, T.217 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.280 NA.31: 6 residues within 4Å: Chain A: S.142, G.143 Chain F: F.210, S.215, G.216, T.217 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.216 NA.37: 6 residues within 4Å: Chain C: S.142, G.143 Chain G: F.210, S.215, G.216, T.217 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.280 NA.43: 6 residues within 4Å: Chain D: S.142, G.143 Chain H: F.210, S.215, G.216, T.217 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.280

8 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 15 residues within 4Å: Chain A: H.154, H.182, G.184, G.185, G.186, R.214, S.254, D.255, A.256, R.257, G.304, L.305, H.307, E.308 Chain G: E.22 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain G Hydrogen bonds: A:H.154, A:H.182, A:G.185, A:G.186, A:S.254, A:A.256, A:G.304, G:E.22, G:R.347 Water bridges: G:R.347 ACP.8: 15 residues within 4Å: Chain B: H.154, H.182, G.184, G.185, G.186, R.214, S.254, D.255, A.256, R.257, G.304, L.305, H.307, E.308 Chain H: E.22 10 PLIP interactions: 3 interactions with chain H, 7 interactions with chain B Hydrogen bonds: H:E.22, H:R.347, B:H.154, B:H.182, B:G.185, B:G.186, B:S.254, B:A.256, B:G.304 Water bridges: H:R.347 ACP.14: 15 residues within 4Å: Chain C: H.154, H.182, G.184, G.185, G.186, R.214, S.254, D.255, A.256, R.257, G.304, L.305, H.307, E.308 Chain E: E.22 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:H.154, C:H.182, C:G.185, C:G.186, C:S.254, C:A.256, C:G.304, E:E.22, E:R.347 Water bridges: E:R.347 ACP.20: 15 residues within 4Å: Chain D: H.154, H.182, G.184, G.185, G.186, R.214, S.254, D.255, A.256, R.257, G.304, L.305, H.307, E.308 Chain F: E.22 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:H.154, D:H.182, D:G.185, D:G.186, D:S.254, D:A.256, D:G.304, F:E.22, F:R.347 Water bridges: F:R.347 ACP.26: 15 residues within 4Å: Chain C: E.22 Chain E: H.154, H.182, G.184, G.185, G.186, R.214, S.254, D.255, A.256, R.257, G.304, L.305, H.307, E.308 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain E Hydrogen bonds: C:E.22, C:R.347, E:H.154, E:H.182, E:G.185, E:G.186, E:S.254, E:A.256, E:G.304 ACP.32: 15 residues within 4Å: Chain D: E.22 Chain F: H.154, H.182, G.184, G.185, G.186, R.214, S.254, D.255, A.256, R.257, G.304, L.305, H.307, E.308 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:H.154, F:H.182, F:G.185, F:G.186, F:S.254, F:A.256, F:G.304, D:E.22, D:R.347 ACP.38: 15 residues within 4Å: Chain A: E.22 Chain G: H.154, H.182, G.184, G.185, G.186, R.214, S.254, D.255, A.256, R.257, G.304, L.305, H.307, E.308 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain A Hydrogen bonds: G:H.154, G:H.182, G:G.185, G:G.186, G:S.254, G:A.256, G:G.304, A:E.22, A:R.347 ACP.44: 15 residues within 4Å: Chain B: E.22 Chain H: H.154, H.182, G.184, G.185, G.186, R.214, S.254, D.255, A.256, R.257, G.304, L.305, H.307, E.308 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain B Hydrogen bonds: H:H.154, H:H.182, H:G.185, H:G.186, H:S.254, H:A.256, H:G.304, B:E.22, B:R.347

32 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: R.74, D.128, H.154, A.155, L.156, E.334 Ligand excluded by PLIP FMT.4: 4 residues within 4Å: Chain A: R.257, R.261 Chain G: F.2, R.347 Ligand excluded by PLIP FMT.5: 3 residues within 4Å: Chain A: N.177, R.193, K.194 Ligand excluded by PLIP FMT.6: 3 residues within 4Å: Chain A: R.275, W.315, R.319 Ligand excluded by PLIP FMT.9: 6 residues within 4Å: Chain B: R.74, D.128, H.154, A.155, L.156, E.334 Ligand excluded by PLIP FMT.10: 4 residues within 4Å: Chain B: R.257, R.261 Chain H: F.2, R.347 Ligand excluded by PLIP FMT.11: 3 residues within 4Å: Chain B: N.177, R.193, K.194 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain B: R.275, W.315, R.319 Ligand excluded by PLIP FMT.15: 6 residues within 4Å: Chain C: R.74, D.128, H.154, A.155, L.156, E.334 Ligand excluded by PLIP FMT.16: 4 residues within 4Å: Chain C: R.257, R.261 Chain E: F.2, R.347 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain C: N.177, R.193, K.194 Ligand excluded by PLIP FMT.18: 3 residues within 4Å: Chain C: R.275, W.315, R.319 Ligand excluded by PLIP FMT.21: 6 residues within 4Å: Chain D: R.74, D.128, H.154, A.155, L.156, E.334 Ligand excluded by PLIP FMT.22: 4 residues within 4Å: Chain D: R.257, R.261 Chain F: F.2, R.347 Ligand excluded by PLIP FMT.23: 3 residues within 4Å: Chain D: N.177, R.193, K.194 Ligand excluded by PLIP FMT.24: 3 residues within 4Å: Chain D: R.275, W.315, R.319 Ligand excluded by PLIP FMT.27: 6 residues within 4Å: Chain E: R.74, D.128, H.154, A.155, L.156, E.334 Ligand excluded by PLIP FMT.28: 4 residues within 4Å: Chain C: F.2, R.347 Chain E: R.257, R.261 Ligand excluded by PLIP FMT.29: 3 residues within 4Å: Chain E: N.177, R.193, K.194 Ligand excluded by PLIP FMT.30: 3 residues within 4Å: Chain E: R.275, W.315, R.319 Ligand excluded by PLIP FMT.33: 6 residues within 4Å: Chain F: R.74, D.128, H.154, A.155, L.156, E.334 Ligand excluded by PLIP FMT.34: 4 residues within 4Å: Chain D: F.2, R.347 Chain F: R.257, R.261 Ligand excluded by PLIP FMT.35: 3 residues within 4Å: Chain F: N.177, R.193, K.194 Ligand excluded by PLIP FMT.36: 3 residues within 4Å: Chain F: R.275, W.315, R.319 Ligand excluded by PLIP FMT.39: 6 residues within 4Å: Chain G: R.74, D.128, H.154, A.155, L.156, E.334 Ligand excluded by PLIP FMT.40: 4 residues within 4Å: Chain A: F.2, R.347 Chain G: R.257, R.261 Ligand excluded by PLIP FMT.41: 3 residues within 4Å: Chain G: N.177, R.193, K.194 Ligand excluded by PLIP FMT.42: 3 residues within 4Å: Chain G: R.275, W.315, R.319 Ligand excluded by PLIP FMT.45: 6 residues within 4Å: Chain H: R.74, D.128, H.154, A.155, L.156, E.334 Ligand excluded by PLIP FMT.46: 4 residues within 4Å: Chain B: F.2, R.347 Chain H: R.257, R.261 Ligand excluded by PLIP FMT.47: 3 residues within 4Å: Chain H: N.177, R.193, K.194 Ligand excluded by PLIP FMT.48: 3 residues within 4Å: Chain H: R.275, W.315, R.319 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diao, J. et al., Crystal structure of butyrate kinase 2 from Thermotoga maritima, a member of the ASKHA superfamily of phosphotransferases. J.Bacteriol. (2009)

Release Date

2005-03-29

Peptides

Probable butyrate kinase 2: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Probable butyrate kinase 2