SMTL ID : 2v9n.1

L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F- E192A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.141, H.143, H.212 Ligands: CIT.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.141, A:H.143, A:H.212 ZN.8: 4 residues within 4Å: Chain B: H.141, H.143, H.212 Ligands: CIT.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.141, B:H.143, B:H.212 ZN.15: 4 residues within 4Å: Chain C: H.141, H.143, H.212 Ligands: CIT.16 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.141, C:H.143, C:H.212 ZN.22: 4 residues within 4Å: Chain D: H.141, H.143, H.212 Ligands: CIT.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.141, D:H.143, D:H.212

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

CIT.2: 13 residues within 4Å: Chain A: N.29, G.30, G.31, N.32, E.117, H.141, H.143, P.188, H.212 Chain C: T.170, E.171 Ligands: ZN.1, PO4.3 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.31, A:N.32, C:E.171 Water bridges: A:N.29, A:E.117, A:H.143, C:E.171 Salt bridges: A:H.141, A:H.141, A:H.143, A:H.212, A:H.212 CIT.9: 13 residues within 4Å: Chain B: N.29, G.30, G.31, N.32, E.117, H.141, H.143, P.188, H.212 Chain D: T.170, E.171 Ligands: ZN.8, PO4.10 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.31, B:N.32, D:E.171 Water bridges: B:N.29, B:E.117, B:H.143, D:E.171 Salt bridges: B:H.141, B:H.141, B:H.143, B:H.212, B:H.212 CIT.16: 14 residues within 4Å: Chain B: T.170, E.171 Chain C: N.29, G.30, G.31, N.32, E.117, H.141, H.143, P.188, W.209, H.212 Ligands: ZN.15, PO4.17 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:G.31, C:N.32, B:E.171, B:E.171 Water bridges: C:N.29, C:E.117, C:H.143, B:E.171 Salt bridges: C:H.141, C:H.141, C:H.143, C:H.212, C:H.212 CIT.23: 14 residues within 4Å: Chain A: T.170, E.171 Chain D: N.29, G.30, G.31, N.32, E.117, H.141, H.143, P.188, W.209, H.212 Ligands: ZN.22, PO4.24 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.31, D:N.32, D:E.117 Water bridges: D:N.29, D:S.116, D:E.117, D:H.143, A:E.171 Salt bridges: D:H.141, D:H.141, D:H.143, D:H.212, D:H.212

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

PO4.3: 8 residues within 4Å: Chain A: N.29, G.31, N.32, S.75, G.76, T.115, S.116 Ligands: CIT.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.29, A:N.29, A:N.32, A:G.76, A:T.115, A:S.116, A:S.116 PO4.4: 4 residues within 4Å: Chain A: T.158, E.200, K.203, H.204 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.158 Water bridges: A:T.158, A:T.158 Salt bridges: A:K.203, A:H.204 PO4.10: 8 residues within 4Å: Chain B: N.29, G.31, N.32, S.75, G.76, T.115, S.116 Ligands: CIT.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.29, B:N.32, B:S.75, B:G.76, B:T.115, B:T.115, B:S.116 Water bridges: B:S.75, B:S.116, B:S.116 PO4.11: 4 residues within 4Å: Chain B: T.158, E.200, K.203, H.204 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.200, B:E.200 Salt bridges: B:H.204 PO4.17: 8 residues within 4Å: Chain C: N.29, G.31, N.32, S.75, G.76, T.115, S.116 Ligands: CIT.16 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.29, C:N.29, C:G.31, C:N.32, C:S.75, C:G.76, C:T.115, C:S.116 PO4.18: 2 residues within 4Å: Chain C: H.46, D.47 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.47 Water bridges: C:F.49, C:F.49 PO4.19: 4 residues within 4Å: Chain C: T.158, E.200, K.203, H.204 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.158 Water bridges: C:H.204 Salt bridges: C:K.203, C:H.204 PO4.24: 8 residues within 4Å: Chain D: N.29, G.31, N.32, S.75, G.76, T.115, S.116 Ligands: CIT.23 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.29, D:N.29, D:N.32, D:G.76, D:T.115, D:S.116, D:S.116 Water bridges: D:S.116, D:S.116 PO4.25: 2 residues within 4Å: Chain D: H.50, Q.51 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.51 Water bridges: D:H.50, D:Q.51, D:Q.52 Salt bridges: D:H.50 PO4.26: 3 residues within 4Å: Chain D: T.158, E.200, H.204 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.158 Salt bridges: D:H.204

8 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.5: 3 residues within 4Å: Chain A: R.80, Q.83, L.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.80, A:R.80, A:Q.83 PGO.6: 4 residues within 4Å: Chain A: V.153, L.154, Y.242 Chain C: M.244 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.244 PGO.12: 2 residues within 4Å: Chain B: R.80, Q.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.80, B:R.80, B:Q.83 PGO.14: 4 residues within 4Å: Chain B: M.244 Chain C: V.153, L.154, Y.242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.244 PGO.20: 3 residues within 4Å: Chain C: R.80, Q.83, L.84 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.80, C:R.80, C:Q.83 PGO.27: 3 residues within 4Å: Chain D: R.80, Q.83, L.84 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.80, D:R.80, D:Q.83 PGO.29: 5 residues within 4Å: Chain A: M.244 Chain D: V.153, L.154, Y.242 Ligands: PGO.30 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.242 PGO.30: 5 residues within 4Å: Chain D: L.154, V.160, Q.164, Y.242 Ligands: PGO.29 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.242

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: T.190, D.191, A.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.191, A:D.191, A:D.191, A:A.192 GOL.13: 4 residues within 4Å: Chain B: T.190, D.191, A.192 Chain D: R.262 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.191, B:D.191, B:A.192 Water bridges: B:D.191, D:R.262 GOL.21: 3 residues within 4Å: Chain B: R.262 Chain C: T.190, D.191 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.191, C:D.191, B:R.262, B:R.262 GOL.28: 3 residues within 4Å: Chain D: T.190, D.191, A.192 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.191, D:A.192 Water bridges: D:D.191 GOL.31: 6 residues within 4Å: Chain A: D.222, E.223 Chain D: G.76, F.78, N.81, F.88 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.222, D:N.81 Water bridges: A:D.222, A:E.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grueninger, D. et al., Designed protein-protein association. Science (2008)

Release Date

2008-01-15

Peptides

RHAMNULOSE-1-PHOSPHATE ALDOLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

RHAMNULOSE-1-PHOSPHATE ALDOLASE

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