SMTL ID : 3vpd.1

LysX from Thermus thermophilus complexed with AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 21 residues within 4Å: Chain A: V.127, K.129, W.135, G.136, L.139, Q.169, E.170, Y.171, V.172, K.174, D.178, R.180, R.194, W.199, I.200, T.201, D.237, F.239, N.248, E.249, N.251 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:K.129, A:W.135, A:W.135, A:G.136, A:E.170, A:V.172, A:D.178, A:D.178, A:R.180, A:R.180, A:R.194, A:R.194, A:T.201, A:D.237, A:N.248, A:E.249, A:E.249, A:N.251 Water bridges: A:K.174 Salt bridges: A:K.129 pi-Stacking: A:W.199 ANP.4: 16 residues within 4Å: Chain B: V.127, K.129, W.135, G.136, L.139, Q.169, E.170, Y.171, V.172, K.174, D.178, R.180, R.194, F.239, N.248, E.249 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.129, B:E.170, B:V.172, B:K.174, B:D.178, B:R.180, B:R.180, B:R.194, B:R.194, B:N.248 Salt bridges: B:K.129 ANP.6: 21 residues within 4Å: Chain C: V.127, K.129, W.135, G.136, L.139, Q.169, E.170, Y.171, V.172, K.174, D.178, R.180, R.194, W.199, I.200, T.201, D.237, F.239, N.248, E.249, N.251 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:K.129, C:W.135, C:W.135, C:G.136, C:E.170, C:V.172, C:D.178, C:R.180, C:R.180, C:R.194, C:R.194, C:T.201, C:N.248, C:E.249, C:N.251 Water bridges: C:K.174 Salt bridges: C:K.129 pi-Stacking: C:W.199 ANP.9: 16 residues within 4Å: Chain D: V.127, K.129, W.135, G.136, L.139, Q.169, E.170, Y.171, V.172, K.174, D.178, R.180, R.194, F.239, N.248, E.249 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.129, D:E.170, D:V.172, D:K.174, D:D.178, D:R.180, D:R.180, D:R.194, D:R.194, D:N.248 Salt bridges: D:K.129

4 x BUA: butanoic acid(Non-covalent)

BUA.2: 6 residues within 4Å: Chain A: T.203, E.255, F.256, K.257, N.258, S.259 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.258, A:N.258, A:S.259, A:S.259 Salt bridges: A:K.257 BUA.5: 5 residues within 4Å: Chain B: E.255, F.256, K.257, N.258, S.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.258, B:N.258, B:S.259 BUA.7: 6 residues within 4Å: Chain C: T.203, E.255, F.256, K.257, N.258, S.259 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.258, C:N.258, C:S.259, C:S.259 Salt bridges: C:K.257 BUA.10: 5 residues within 4Å: Chain D: E.255, F.256, K.257, N.258, S.259 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.258, D:N.258, D:S.259

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

CIT.3: 7 residues within 4Å: Chain A: V.57, S.58, Q.59, S.60, G.133, W.135 Chain B: F.161 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.161, A:W.135 Hydrogen bonds: A:V.57, A:Q.59, A:S.60 Water bridges: A:Q.59, A:R.61, A:S.134 CIT.8: 7 residues within 4Å: Chain C: V.57, S.58, Q.59, S.60, G.133, W.135 Chain D: F.161 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.135, D:F.161 Hydrogen bonds: C:V.57, C:Q.59, C:S.60 Water bridges: C:Q.59, C:R.61, C:S.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ouchi, T. et al., Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat.Chem.Biol. (2013)

Release Date

2013-02-27

Peptides

Ribosomal protein S6 modification protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Ribosomal protein S6 modification protein