SMTL ID : 2iss.1

Structure of the PLP synthase Holoenzyme from Thermotoga maritima

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-12-12-mer

Ligands

12 x 5RP: RIBULOSE-5-PHOSPHATE(Post Translational Modification)

5RP.1: 15 residues within 4Å: Chain A: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.102 Hydrogen bonds: A:D.45, A:K.102, A:R.168, A:G.174, A:G.234, A:G.235, A:G.256, A:S.257 5RP.3: 15 residues within 4Å: Chain B: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:K.102 Hydrogen bonds: B:D.45, B:K.102, B:R.168, B:G.174, B:G.234, B:G.235, B:G.256, B:S.257 5RP.5: 15 residues within 4Å: Chain C: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:K.102 Hydrogen bonds: C:D.45, C:K.102, C:R.168, C:G.174, C:G.234, C:G.235, C:G.256, C:S.257 5RP.7: 15 residues within 4Å: Chain G: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:K.102 Hydrogen bonds: G:D.45, G:K.102, G:R.168, G:G.174, G:G.234, G:G.235, G:G.256, G:S.257 5RP.9: 15 residues within 4Å: Chain H: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:K.102 Hydrogen bonds: H:D.45, H:K.102, H:R.168, H:G.174, H:G.234, H:G.235, H:G.256, H:S.257 5RP.11: 15 residues within 4Å: Chain I: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:K.102 Hydrogen bonds: I:D.45, I:K.102, I:R.168, I:G.174, I:G.234, I:G.235, I:G.256, I:S.257 5RP.13: 15 residues within 4Å: Chain M: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain M Hydrophobic interactions: M:K.102 Hydrogen bonds: M:D.45, M:K.102, M:R.168, M:G.174, M:G.234, M:G.235, M:G.256, M:S.257 5RP.15: 15 residues within 4Å: Chain N: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:K.102 Hydrogen bonds: N:D.45, N:K.102, N:R.168, N:G.174, N:G.234, N:G.235, N:G.256, N:S.257 5RP.17: 15 residues within 4Å: Chain O: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain O Hydrophobic interactions: O:K.102 Hydrogen bonds: O:D.45, O:K.102, O:R.168, O:G.174, O:G.234, O:G.235, O:G.256, O:S.257 5RP.19: 15 residues within 4Å: Chain S: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain S Hydrophobic interactions: S:K.102 Hydrogen bonds: S:D.45, S:K.102, S:R.168, S:G.174, S:G.234, S:G.235, S:G.256, S:S.257 5RP.21: 15 residues within 4Å: Chain T: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain T Hydrophobic interactions: T:K.102 Hydrogen bonds: T:D.45, T:K.102, T:R.168, T:G.174, T:G.234, T:G.235, T:G.256, T:S.257 5RP.23: 15 residues within 4Å: Chain U: D.45, M.64, P.70, K.102, D.123, V.127, R.168, E.172, A.173, G.174, G.234, G.235, F.254, G.256, S.257 9 PLIP interactions: 9 interactions with chain U Hydrophobic interactions: U:K.102 Hydrogen bonds: U:D.45, U:K.102, U:R.168, U:G.174, U:G.234, U:G.235, U:G.256, U:S.257

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

PO4.2: 5 residues within 4Å: Chain A: H.136, E.155, R.158, R.159 Chain G: K.208 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain G Salt bridges: A:R.158, A:R.159, G:K.208 PO4.4: 5 residues within 4Å: Chain B: H.136, E.155, R.158, R.159 Chain O: K.208 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain O Salt bridges: B:R.158, B:R.159, O:K.208 PO4.6: 5 residues within 4Å: Chain C: H.136, E.155, R.158, R.159 Chain N: K.208 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain C Salt bridges: N:K.208, C:R.158, C:R.159 PO4.8: 5 residues within 4Å: Chain A: K.208 Chain G: H.136, E.155, R.158, R.159 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain G Salt bridges: A:K.208, G:R.158, G:R.159 PO4.10: 5 residues within 4Å: Chain H: H.136, E.155, R.158, R.159 Chain U: K.208 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain U Salt bridges: H:R.158, H:R.159, U:K.208 PO4.12: 5 residues within 4Å: Chain I: H.136, E.155, R.158, R.159 Chain T: K.208 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain T Salt bridges: I:R.158, I:R.159, T:K.208 PO4.14: 5 residues within 4Å: Chain M: H.136, E.155, R.158, R.159 Chain S: K.208 3 PLIP interactions: 1 interactions with chain S, 2 interactions with chain M Salt bridges: S:K.208, M:R.158, M:R.159 PO4.16: 5 residues within 4Å: Chain C: K.208 Chain N: H.136, E.155, R.158, R.159 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain C Salt bridges: N:R.158, N:R.159, C:K.208 PO4.18: 5 residues within 4Å: Chain B: K.208 Chain O: H.136, E.155, R.158, R.159 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain O Salt bridges: B:K.208, O:R.158, O:R.159 PO4.20: 5 residues within 4Å: Chain M: K.208 Chain S: H.136, E.155, R.158, R.159 3 PLIP interactions: 2 interactions with chain S, 1 interactions with chain M Salt bridges: S:R.158, S:R.159, M:K.208 PO4.22: 5 residues within 4Å: Chain I: K.208 Chain T: H.136, E.155, R.158, R.159 3 PLIP interactions: 2 interactions with chain T, 1 interactions with chain I Salt bridges: T:R.158, T:R.159, I:K.208 PO4.24: 5 residues within 4Å: Chain H: K.208 Chain U: H.136, E.155, R.158, R.159 3 PLIP interactions: 2 interactions with chain U, 1 interactions with chain H Salt bridges: U:R.158, U:R.159, H:K.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zein, F. et al., Structural Insights into the Mechanism of the PLP Synthase Holoenzyme from Thermotoga maritima. Biochemistry (2006)

Release Date

2007-01-02

Peptides

Pyridoxal biosynthesis lyase pdxS: ABCGHIMNOSTU
Glutamine amidotransferase subunit pdxT: DEFJKLPQRVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

G
A

H
B

I
C

M
A

N
B

O
C

S
A

T
B

U
C

D
D

E
E

F
F

J
D

K
E

L
F

P
D

Q
E

R
F

V
D

W
E

X
F

Pyridoxal biosynthesis lyase pdxS

Glutamine amidotransferase subunit pdxT