SMTL ID : 8u7j.1

Crystal Structure of Staphylococcus aureus PLP synthase complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

hetero-12-12-mer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: H.118, R.140, R.141 Chain C: K.190 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.118, A:R.140, A:R.141 PO4.3: 4 residues within 4Å: Chain A: K.190 Chain C: H.118, R.140, R.141 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Salt bridges: C:H.118, C:R.140, C:R.141, A:K.190 PO4.4: 5 residues within 4Å: Chain D: H.118, E.137, R.140, R.141 Chain K: K.190 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:H.118, D:R.140, D:R.141 PO4.5: 4 residues within 4Å: Chain E: H.118, R.140, R.141 Chain G: K.190 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:H.118, E:R.140, E:R.141 PO4.6: 5 residues within 4Å: Chain F: H.118, E.137, R.140, R.141 Chain M: K.190 3 PLIP interactions: 3 interactions with chain F Salt bridges: F:H.118, F:R.140, F:R.141 PO4.7: 5 residues within 4Å: Chain E: K.190 Chain G: H.118, E.137, R.140, R.141 3 PLIP interactions: 3 interactions with chain G Salt bridges: G:H.118, G:R.140, G:R.141 PO4.9: 5 residues within 4Å: Chain I: H.118, E.137, R.140, R.141 Chain J: K.190 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:E.137, I:E.137 Salt bridges: I:H.118, I:R.140, I:R.141 PO4.10: 5 residues within 4Å: Chain I: K.190 Chain J: H.118, E.137, R.140, R.141 3 PLIP interactions: 3 interactions with chain J Salt bridges: J:H.118, J:R.140, J:R.141 PO4.11: 4 residues within 4Å: Chain D: K.190 Chain K: H.118, R.140, R.141 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain K Salt bridges: D:K.190, K:H.118, K:R.140, K:R.141 PO4.12: 4 residues within 4Å: Chain L: H.118, E.137, R.140, R.141 3 PLIP interactions: 3 interactions with chain L Salt bridges: L:H.118, L:R.140, L:R.141 PO4.13: 3 residues within 4Å: Chain M: H.118, R.140, R.141 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain F Salt bridges: M:H.118, M:R.140, M:R.141, F:K.190

12 x GLN: GLUTAMINE(Non-covalent)

GLN.2: 12 residues within 4Å: Chain B: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 Chain C: M.19, S.78 10 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:R.132 Hydrogen bonds: B:G.48, B:E.49, B:S.50, B:R.103, B:N.104, B:R.132, Q.2, Q.2 Salt bridges: B:R.103 GLN.14: 11 residues within 4Å: Chain D: M.19 Chain N: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 10 PLIP interactions: 8 interactions with chain N, 2 Ligand-Ligand interactions Hydrophobic interactions: N:R.132 Hydrogen bonds: N:G.48, N:G.48, N:E.49, N:S.50, N:R.103, N:R.132, Q.14, Q.14 Salt bridges: N:R.103 GLN.15: 11 residues within 4Å: Chain E: M.19 Chain O: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 11 PLIP interactions: 9 interactions with chain O, 2 Ligand-Ligand interactions Hydrophobic interactions: O:R.132 Hydrogen bonds: O:G.48, O:G.48, O:E.49, O:S.50, O:R.103, O:N.104, O:R.132, Q.15, Q.15 Salt bridges: O:R.103 GLN.16: 12 residues within 4Å: Chain F: M.19, S.78 Chain P: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 10 PLIP interactions: 2 Ligand-Ligand interactions, 8 interactions with chain P Hydrogen bonds: Q.16, Q.16, P:G.48, P:G.48, P:E.49, P:S.50, P:R.103, P:R.132 Hydrophobic interactions: P:R.132 Salt bridges: P:R.103 GLN.17: 11 residues within 4Å: Chain G: M.19 Chain Q: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 11 PLIP interactions: 9 interactions with chain Q, 2 Ligand-Ligand interactions Hydrophobic interactions: Q:R.132 Hydrogen bonds: Q:G.48, Q:E.49, Q:S.50, Q:R.103, Q:N.104, Q:N.104, Q:R.132, Q.17, Q.17 Salt bridges: Q:R.103 GLN.18: 12 residues within 4Å: Chain H: M.19, S.78 Chain R: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 11 PLIP interactions: 9 interactions with chain R, 2 Ligand-Ligand interactions Hydrophobic interactions: R:R.132 Hydrogen bonds: R:G.48, R:G.48, R:E.49, R:S.50, R:R.103, R:N.104, R:R.132, Q.18, Q.18 Salt bridges: R:R.103 GLN.19: 12 residues within 4Å: Chain I: M.19, S.78 Chain S: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 10 PLIP interactions: 8 interactions with chain S, 2 Ligand-Ligand interactions Hydrophobic interactions: S:R.132 Hydrogen bonds: S:G.48, S:G.48, S:E.49, S:S.50, S:R.103, S:R.132, Q.19, Q.19 Salt bridges: S:R.103 GLN.20: 12 residues within 4Å: Chain A: M.19, S.78 Chain T: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 10 PLIP interactions: 8 interactions with chain T, 2 Ligand-Ligand interactions Hydrophobic interactions: T:R.132 Hydrogen bonds: T:G.48, T:G.48, T:E.49, T:S.50, T:R.103, T:R.132, Q.20, Q.20 Salt bridges: T:R.103 GLN.21: 12 residues within 4Å: Chain J: M.19, S.78 Chain U: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 10 PLIP interactions: 8 interactions with chain U, 2 Ligand-Ligand interactions Hydrophobic interactions: U:R.132 Hydrogen bonds: U:G.48, U:E.49, U:S.50, U:R.103, U:N.104, U:R.132, Q.21, Q.21 Salt bridges: U:R.103 GLN.22: 12 residues within 4Å: Chain K: M.19, S.78 Chain V: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 10 PLIP interactions: 8 interactions with chain V, 2 Ligand-Ligand interactions Hydrophobic interactions: V:R.132 Hydrogen bonds: V:G.48, V:E.49, V:S.50, V:R.103, V:N.104, V:R.132, Q.22, Q.22 Salt bridges: V:R.103 GLN.23: 12 residues within 4Å: Chain L: M.19, S.78 Chain W: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 10 PLIP interactions: 8 interactions with chain W, 2 Ligand-Ligand interactions Hydrophobic interactions: W:R.132 Hydrogen bonds: W:G.48, W:E.49, W:S.50, W:R.103, W:N.104, W:R.132, Q.23, Q.23 Salt bridges: W:R.103 GLN.24: 11 residues within 4Å: Chain M: M.19 Chain X: G.48, E.49, S.50, C.77, A.78, I.81, R.103, N.104, I.131, R.132 10 PLIP interactions: 8 interactions with chain X, 2 Ligand-Ligand interactions Hydrophobic interactions: X:R.132 Hydrogen bonds: X:G.48, X:E.49, X:S.50, X:R.103, X:N.104, X:N.104, Q.24, Q.24 Salt bridges: X:R.103

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 3 residues within 4Å: Chain H: H.118, R.140, R.141 3 PLIP interactions: 3 interactions with chain H Salt bridges: H:H.118, H:R.140, H:R.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barra, A.L.C. et al., Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface. J.Biol.Chem. (2024)

Release Date

2024-07-24

Peptides

Pyridoxal 5'-phosphate synthase subunit PdxS: ACDEFGHIJKLM
Pyridoxal 5'-phosphate synthase subunit PdxT: BNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
G

D
B

E
L

F
K

G
F

H
J

I
C

J
I

K
H

L
D

M
E

B
T

N
N

O
S

P
X

Q
R

R
W

S
O

T
M

U
V

V
U

W
P

X
Q

Pyridoxal 5'-phosphate synthase subunit PdxS

Pyridoxal 5'-phosphate synthase subunit PdxT

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