SMTL ID : 1x9j.1 (4 other biounits)

Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-octamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: V.130, F.153, H.154, A.203, L.204, R.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.153, A:H.154, A:R.214, A:R.214 GOL.3: 5 residues within 4Å: Chain A: R.23 Chain B: H.307, G.331, S.332, N.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.307, B:S.332 GOL.4: 5 residues within 4Å: Chain C: M.1, R.3, S.67, F.68, S.69 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.3, C:R.3, C:F.68 GOL.8: 5 residues within 4Å: Chain D: M.1, R.3, S.67, F.68, S.69 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.3, D:S.69 GOL.12: 6 residues within 4Å: Chain F: M.1, R.3, S.66, S.67, F.68, S.69 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.3, F:R.3

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

PO4.2: 7 residues within 4Å: Chain B: T.217, W.284, K.287 Chain C: D.207, T.217, W.284, K.287 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.207, C:T.217 Salt bridges: C:K.287, B:K.287 PO4.9: 8 residues within 4Å: Chain D: D.207, T.217, W.284, K.287 Chain E: D.207, T.217, W.284, K.287 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:T.217, E:T.217, D:W.284 Salt bridges: E:K.287, D:K.287 PO4.10: 3 residues within 4Å: Chain E: K.97, H.114, R.115 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.114 Salt bridges: E:K.97, E:R.115 PO4.11: 7 residues within 4Å: Chain F: D.207, T.217, W.284, K.287 Chain G: T.217, W.284, K.287 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:D.207, G:T.217 Salt bridges: F:K.287, G:K.287 PO4.15: 7 residues within 4Å: Chain A: D.207, T.217, W.284, K.287 Chain H: T.217, W.284, K.287 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain H Hydrogen bonds: A:T.217 Salt bridges: A:K.287, H:K.287

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

NA.5: 5 residues within 4Å: Chain D: V.58, E.59, T.61, G.62, Y.63 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.58, D:T.61, D:Y.63

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 11 residues within 4Å: Chain D: S.11, H.104, H.154, H.182, G.184, G.185, G.186, A.203, L.204, R.214, E.334 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.11, D:S.11, D:G.185, D:G.186, D:E.334 Salt bridges: D:H.104, D:H.104, D:H.154, D:H.154, D:H.182, D:R.214, D:R.214 CIT.7: 8 residues within 4Å: Chain C: R.23 Chain D: S.13, K.15, N.29, G.304, H.307, G.331, S.332 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.15 Hydrogen bonds: D:S.13, D:S.13, D:N.29, D:S.332 Salt bridges: D:K.15 CIT.13: 10 residues within 4Å: Chain G: S.11, H.104, V.130, H.154, H.182, G.184, G.185, G.186, R.214 Ligands: CIT.14 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:S.11, G:S.11, G:G.185, G:G.186 Salt bridges: G:H.104, G:H.104, G:H.154, G:H.154, G:H.182, G:R.214 CIT.14: 9 residues within 4Å: Chain G: K.15, N.29, H.182, G.304, H.307, G.331, S.332, E.334 Ligands: CIT.13 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:N.29, G:G.304, G:S.332, G:S.332, G:S.332, G:E.334 Salt bridges: G:K.15, G:H.182, G:H.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diao, J.S. et al., Structure of butyrate kinase 2 reveals both open and closed conformations of the two domains: implications for substrate-induced changes. To be Published

Release Date

2005-08-30

Peptides

Probable butyrate kinase 2: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Probable butyrate kinase 2

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