SMTL ID : 6nzy.1

Structural Determination of the Carboxy-terminal portion of ATP-citrate lyase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

2 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 9 residues within 4Å: Chain A: L.130, K.134, P.139, V.140, I.143, T.185, K.188, K.189, L.192 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.140, A:I.143 Salt bridges: A:K.134, A:K.188, A:K.189, A:K.189 ACO.21: 10 residues within 4Å: Chain D: L.130, K.134, P.139, V.140, I.143, G.144, T.185, K.188, K.189, L.192 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.134, D:V.140, D:V.140 Salt bridges: D:K.134, D:K.134, D:K.188, D:K.189

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

PO4.2: 7 residues within 4Å: Chain A: H.69, V.73, F.104, F.218, R.222 Ligands: GOL.6, GOL.8 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.69, A:R.222 PO4.14: 5 residues within 4Å: Chain B: H.69, V.73, F.104, F.218, R.222 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.69, B:R.222 PO4.16: 6 residues within 4Å: Chain C: H.69, V.73, F.104, F.218, R.222 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.69, C:R.222 PO4.22: 6 residues within 4Å: Chain D: H.69, V.73, F.104, F.218, R.222 Ligands: GOL.25 5 PLIP interactions: 5 interactions with chain D Water bridges: D:G.105, D:G.105, D:G.105 Salt bridges: D:H.69, D:R.222

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: I.87, D.88, Q.91 Chain D: G.86, I.87, D.88, P.90, Q.91 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:D.88, D:D.88, D:Q.91 Water bridges: D:G.86, D:D.88 GOL.4: 6 residues within 4Å: Chain A: R.22, E.30 Chain D: E.255, Q.256, E.257 Ligands: GOL.5 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:R.22, A:R.22, D:E.255, D:Q.256 Water bridges: D:V.258 GOL.5: 8 residues within 4Å: Chain A: E.19, E.20, R.22, A.27, S.29, E.30 Chain C: Q.155 Ligands: GOL.4 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A, 1 interactions with chain D Water bridges: C:Q.155, A:R.22, D:E.255 Hydrogen bonds: A:R.22, A:E.30 GOL.6: 9 residues within 4Å: Chain A: R.103, F.104, G.105, G.106, A.107, V.108, D.197 Chain B: L.240 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.103, A:G.105, A:A.107 GOL.7: 8 residues within 4Å: Chain A: P.153, V.157, K.158, V.161, L.179, E.182, I.193, L.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.182 GOL.8: 11 residues within 4Å: Chain A: I.65, S.66, H.69, V.108, R.156, V.196, D.197, I.200, F.218, R.222 Ligands: PO4.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.66, A:R.156, A:D.197, A:R.222, A:R.222 Water bridges: A:I.65, A:S.66, A:R.156 GOL.9: 6 residues within 4Å: Chain A: R.10, T.12, K.48 Chain C: D.232, N.235, Q.236 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:D.232, C:N.235, A:R.10, A:R.10, A:K.48 GOL.10: 5 residues within 4Å: Chain A: T.52, E.54, E.55, S.169, L.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.54, A:E.55, A:E.55 GOL.17: 7 residues within 4Å: Chain B: I.87, D.88, Q.91 Chain C: G.86, I.87, D.88, Q.91 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.88, C:D.88, C:Q.91 GOL.18: 11 residues within 4Å: Chain C: I.65, S.66, H.69, V.108, R.156, V.196, D.197, I.200, F.218, R.222 Ligands: PO4.16 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.69, C:R.156, C:R.156, C:D.197, C:D.197, C:R.222, C:R.222 Water bridges: C:I.65 GOL.23: 9 residues within 4Å: Chain A: K.253, Q.256 Chain D: A.24, G.25, Y.26, L.44, K.48, K.49, L.50 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:K.253, A:Q.256, D:Y.26, D:Y.26, D:L.50 Water bridges: A:Q.256 GOL.24: 6 residues within 4Å: Chain B: D.232, N.235, Q.236 Chain D: R.10, T.12, K.48 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:D.232, B:D.232, D:R.10, D:K.48 Water bridges: B:N.235 GOL.25: 11 residues within 4Å: Chain D: I.65, S.66, H.69, V.108, R.156, V.196, D.197, I.200, F.218, R.222 Ligands: PO4.22 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.66, D:R.156, D:R.156, D:D.197, D:D.197, D:R.222, D:R.222 Water bridges: D:I.65 GOL.26: 5 residues within 4Å: Chain A: E.255, Q.256, E.257 Chain D: R.22, E.30 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:E.255, A:Q.256, D:R.22, D:R.22 Water bridges: A:V.258

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

NA.11: 5 residues within 4Å: Chain A: D.88, M.89, P.90, W.230 Chain C: N.215 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.88, A:M.89, C:N.215 NA.12: 7 residues within 4Å: Chain A: D.15, D.16, R.17 Chain C: G.70, P.71 Chain D: R.242, Y.250 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Water bridges: C:A.72 Hydrogen bonds: D:R.242, D:Y.250, A:D.16 NA.13: 8 residues within 4Å: Chain A: R.242, Y.250 Chain B: G.70, P.71, A.72 Chain D: D.15, D.16, R.17 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.242, D:D.16, D:D.16 NA.15: 4 residues within 4Å: Chain B: K.165, H.171, T.172, D.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.171, B:T.172 NA.19: 5 residues within 4Å: Chain A: N.215 Chain C: D.88, M.89, P.90, W.230 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.88, C:M.89, A:N.215 NA.20: 4 residues within 4Å: Chain C: G.86, I.87, D.88, W.230 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.88 Water bridges: C:W.230 NA.27: 3 residues within 4Å: Chain A: G.18, R.22 Chain D: E.255 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.255, D:E.255 Water bridges: A:G.18 NA.28: 3 residues within 4Å: Chain D: V.157, L.179, E.182 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, V.H. et al., Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion. Protein Sci. (2019)

Release Date

2019-12-18

Peptides

ATP-citrate lyase alpha-subunit: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ATP-citrate lyase alpha-subunit