SMTL ID : 5k2m.1 (2 other biounits)

Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-8-6-mer

Ligands

8 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 27 residues within 4Å: Chain A: K.83, V.120, K.122, G.126, S.127, W.128, G.129, R.130, L.132, Q.162, E.163, F.164, V.165, K.167, D.171, R.187, W.192, I.193, T.194, N.195, D.229, F.231, N.240, E.241 Ligands: PO4.2, MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.122, A:S.127, A:W.128, A:G.129, A:R.130, A:E.163, A:V.165, A:D.171, A:T.194, A:N.195, A:N.240 Water bridges: A:K.83, A:G.126, A:R.187, A:R.187, A:N.243 Salt bridges: A:K.83, A:K.83, A:K.122 ADP.5: 27 residues within 4Å: Chain B: K.83, V.120, K.122, G.126, S.127, W.128, G.129, R.130, L.132, Q.162, E.163, F.164, V.165, K.167, D.171, R.187, W.192, I.193, T.194, N.195, D.229, F.231, N.240, E.241 Ligands: PO4.6, MG.7, MG.8 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.122, B:S.127, B:W.128, B:G.129, B:R.130, B:E.163, B:V.165, B:K.167, B:D.171, B:T.194, B:N.195, B:N.195, B:N.240 Water bridges: B:K.83, B:R.187, B:R.187 Salt bridges: B:K.83, B:K.83, B:K.122 ADP.9: 24 residues within 4Å: Chain C: K.83, V.120, K.122, G.126, S.127, W.128, G.129, L.132, Q.162, E.163, F.164, V.165, K.167, D.171, R.187, W.192, I.193, T.194, N.195, D.229, F.231, N.240, E.241 Ligands: SO4.10 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:K.122, C:S.127, C:G.129, C:R.130, C:E.163, C:V.165, C:D.171, C:T.194, C:N.195, C:N.240, C:E.241 Salt bridges: C:K.83, C:K.83, C:K.122 ADP.11: 23 residues within 4Å: Chain D: K.83, V.120, K.122, G.126, S.127, W.128, G.129, L.132, Q.162, E.163, F.164, V.165, K.167, D.171, R.187, W.192, I.193, T.194, N.195, D.229, F.231, N.240, E.241 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:K.122, D:S.127, D:E.163, D:V.165, D:D.171, D:T.194, D:D.229, D:N.240 Water bridges: D:N.243 Salt bridges: D:K.83, D:K.83, D:K.122 ADP.14: 25 residues within 4Å: Chain G: K.83, V.120, K.122, G.126, S.127, W.128, G.129, L.132, Q.162, E.163, F.164, V.165, K.167, D.171, R.187, W.192, I.193, T.194, N.195, D.229, F.231, N.240, E.241 Ligands: PO4.15, MG.16 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:K.122, G:S.127, G:G.129, G:R.130, G:E.163, G:V.165, G:D.171, G:T.194, G:N.195, G:N.195, G:D.229, G:D.229, G:N.240, G:E.241 Salt bridges: G:K.83, G:K.83, G:K.122 ADP.17: 26 residues within 4Å: Chain H: K.83, V.120, K.122, G.126, S.127, W.128, G.129, L.132, Q.162, E.163, F.164, V.165, K.167, D.171, R.187, W.192, I.193, T.194, N.195, D.229, F.231, N.240, E.241 Ligands: SO4.18, MG.19, MG.20 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:K.122, H:W.128, H:G.129, H:E.163, H:V.165, H:D.171, H:T.194, H:N.195, H:N.195, H:N.240 Water bridges: H:R.130, H:R.130 Salt bridges: H:K.83, H:K.83, H:K.122 ADP.21: 25 residues within 4Å: Chain I: K.83, V.120, K.122, G.126, S.127, W.128, G.129, L.132, Q.162, E.163, F.164, V.165, K.167, D.171, R.187, W.192, I.193, T.194, N.195, D.229, F.231, N.240, E.241, N.243 Ligands: PO4.22 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:K.122, I:S.127, I:W.128, I:E.163, I:V.165, I:D.171, I:T.194, I:N.195, I:N.195, I:D.229, I:D.229, I:N.240, I:N.243 Water bridges: I:R.173 Salt bridges: I:K.83, I:K.83, I:K.122 ADP.24: 26 residues within 4Å: Chain J: K.83, V.120, K.122, G.126, S.127, W.128, G.129, L.132, Q.162, E.163, F.164, V.165, K.167, D.171, R.187, W.192, I.193, T.194, N.195, D.229, F.231, N.240, E.241 Ligands: PO4.25, MG.26, MG.27 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:K.122, J:S.127, J:G.129, J:R.130, J:E.163, J:V.165, J:D.171, J:T.194, J:N.195, J:N.240 Water bridges: J:R.187, J:R.187 Salt bridges: J:K.83, J:K.83, J:K.122

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

PO4.2: 12 residues within 4Å: Chain A: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243 Chain E: E.53 Ligands: ADP.1, MG.3, MG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.128, A:R.187, A:N.243 Water bridges: A:R.187 Salt bridges: A:R.173 PO4.6: 12 residues within 4Å: Chain B: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243 Chain F: E.53 Ligands: ADP.5, MG.7, MG.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.127, B:W.128, B:R.187, B:N.195, B:N.195, B:N.243 Water bridges: B:R.187 Salt bridges: B:R.173 PO4.15: 11 residues within 4Å: Chain G: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243 Chain K: E.53 Ligands: ADP.14, MG.16 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:S.127, G:S.127, G:W.128, G:D.229, G:E.241, G:N.243 Salt bridges: G:R.173, G:R.187 PO4.22: 10 residues within 4Å: Chain I: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243 Ligands: ADP.21, UN1.23 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:S.127, I:S.127, I:W.128, I:R.187, I:N.243 Water bridges: I:R.173 Salt bridges: I:R.173 PO4.25: 12 residues within 4Å: Chain J: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243 Chain N: E.53 Ligands: ADP.24, MG.26, MG.27 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:W.128, J:R.187, J:N.195, J:N.243 Water bridges: J:R.187 Salt bridges: J:R.173

9 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: N.195, D.229, E.241 Ligands: ADP.1, PO4.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.229, A:E.241, H2O.1 MG.4: 6 residues within 4Å: Chain A: S.127, E.241, N.243 Ligands: ADP.1, PO4.2, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.241, A:E.241, H2O.1 MG.7: 6 residues within 4Å: Chain B: N.195, D.229, E.241 Ligands: ADP.5, PO4.6, MG.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.229, B:E.241, H2O.5 MG.8: 6 residues within 4Å: Chain B: S.127, E.241, N.243 Ligands: ADP.5, PO4.6, MG.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.241, B:E.241, H2O.5 MG.16: 6 residues within 4Å: Chain G: R.187, N.195, D.229, E.241 Ligands: ADP.14, PO4.15 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.229, G:E.241 MG.19: 5 residues within 4Å: Chain H: R.187, D.229, E.241 Ligands: ADP.17, SO4.18 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.229, H:E.241 MG.20: 7 residues within 4Å: Chain H: K.83, G.126, S.127, E.241, N.243 Ligands: ADP.17, SO4.18 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.241, H:E.241, H2O.17 MG.26: 5 residues within 4Å: Chain J: D.229, E.241 Ligands: ADP.24, PO4.25, MG.27 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.229, J:E.241, H2O.22 MG.27: 6 residues within 4Å: Chain J: K.83, E.241, N.243 Ligands: ADP.24, PO4.25, MG.26 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.241, J:E.241, H2O.22

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

SO4.10: 8 residues within 4Å: Chain C: S.127, W.128, R.173, R.187, N.195, E.241, N.243 Ligands: ADP.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:W.128, C:R.187, C:R.187, C:N.195, C:E.241, C:E.241, C:N.243 Salt bridges: C:R.173 SO4.18: 12 residues within 4Å: Chain H: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243 Chain L: E.53 Ligands: ADP.17, MG.19, MG.20 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:W.128, H:N.195, H:N.243 Salt bridges: H:R.173, H:R.187

2 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain E: C.4, C.7, C.24, C.27 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.4, E:C.7, E:C.24, E:C.27 ZN.13: 4 residues within 4Å: Chain F: C.4, C.7, C.24, C.27 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.4, F:C.24, F:C.27

1 x UN1: 2-AMINOHEXANEDIOIC ACID(Non-covalent)

UN1.23: 13 residues within 4Å: Chain I: W.128, R.173, Y.175, R.187, N.195, T.196, A.197, E.247, F.248, K.249, N.250, A.251 Ligands: PO4.22 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:T.196, I:E.247 Hydrogen bonds: I:W.128, I:T.196, I:T.196, I:T.196, I:A.197, I:E.247, I:N.250, I:N.250, I:A.251 Salt bridges: I:R.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, A. et al., Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System. J. Biol. Chem. (2016)

Release Date

2016-09-07

Peptides

RimK-related lysine biosynthesis protein: ABCDGHIJ
Probable lysine biosynthesis protein: EFKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

G
G

H
H

I
I

J
J

E
E

F
F

K
K

L
L

M
M

N
N

RimK-related lysine biosynthesis protein

Probable lysine biosynthesis protein

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