SMTL ID : 3und.1

Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x A5P: ARABINOSE-5-PHOSPHATE(Non-covalent)

A5P.1: 16 residues within 4Å: Chain A: N.28, K.62, N.64, R.65, S.66, H.204, Q.207, R.209, A.215, S.216, C.251, D.252 Chain C: R.122 Ligands: PEP.2, KD0.3, EDO.5 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.28, A:K.62, A:N.64, A:N.64, A:S.66, A:S.66, A:Q.207, A:S.216, A:D.252 Water bridges: A:R.65, A:S.67, A:S.67, A:R.170, A:S.216, A:D.252 Salt bridges: A:R.65, A:R.209, C:R.122 A5P.6: 16 residues within 4Å: Chain B: N.28, K.62, N.64, R.65, S.66, H.204, Q.207, R.209, A.215, S.216, C.251, D.252 Chain D: R.122 Ligands: PEP.7, KD0.8, EDO.10 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.28, B:K.62, B:N.64, B:N.64, B:S.66, B:Q.207, B:S.216 Water bridges: B:S.67, B:S.70, B:R.170 Salt bridges: B:R.65, B:R.209, D:R.122 A5P.11: 16 residues within 4Å: Chain A: R.122 Chain C: N.28, K.62, N.64, R.65, S.66, H.204, Q.207, R.209, A.215, S.216, C.251, D.252 Ligands: PEP.12, KD0.13, EDO.15 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.28, C:K.62, C:N.64, C:N.64, C:S.66, C:S.66, C:Q.207, C:S.216, A:R.122 Water bridges: C:R.65, C:S.67, C:R.170 Salt bridges: C:R.65, C:R.209, A:R.122 A5P.16: 15 residues within 4Å: Chain B: R.122 Chain D: N.28, K.62, N.64, R.65, S.66, H.204, Q.207, R.209, A.215, S.216, C.251, D.252 Ligands: PEP.17, KD0.18 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.28, D:K.62, D:N.64, D:N.64, D:S.66, D:H.204, D:Q.207, D:S.216 Water bridges: D:R.65, D:R.65, D:R.170, D:R.170, D:S.216, D:D.252 Salt bridges: D:R.65, D:R.209, B:R.122

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 15 residues within 4Å: Chain A: K.57, S.59, K.62, D.97, Q.115, P.117, A.118, K.140, R.170, H.204, F.239, E.241 Ligands: A5P.1, KD0.3, EDO.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.59, A:S.59, A:Q.115, A:A.118 Water bridges: A:N.64, A:Q.143, A:R.170 Salt bridges: A:K.57, A:K.62, A:K.140, A:K.140, A:R.170, A:H.204, A:H.204 PEP.7: 15 residues within 4Å: Chain B: K.57, S.59, K.62, D.97, Q.115, P.117, A.118, K.140, R.170, H.204, F.239, E.241 Ligands: A5P.6, KD0.8, EDO.10 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.59, B:S.59, B:Q.115, B:A.118 Water bridges: B:N.64, B:N.64, B:N.64, B:D.97 Salt bridges: B:K.57, B:K.62, B:K.140, B:K.140, B:R.170, B:H.204, B:H.204 PEP.12: 15 residues within 4Å: Chain C: K.57, S.59, K.62, D.97, Q.115, P.117, A.118, K.140, R.170, H.204, F.239, E.241 Ligands: A5P.11, KD0.13, EDO.15 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.59, C:D.97, C:Q.115, C:A.118, C:E.241 Water bridges: C:N.64, C:F.119, C:Q.143, C:R.170 Salt bridges: C:K.57, C:K.62, C:K.140, C:K.140, C:R.170, C:H.204, C:H.204 PEP.17: 14 residues within 4Å: Chain D: K.57, S.59, K.62, D.97, Q.115, P.117, A.118, K.140, R.170, H.204, F.239, E.241 Ligands: A5P.16, KD0.18 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.59, D:Q.115, D:A.118 Water bridges: D:N.64, D:D.97, D:D.97, D:R.170, D:R.170, D:R.170 Salt bridges: D:K.57, D:K.62, D:K.140, D:K.140, D:R.170, D:H.204, D:H.204

4 x KD0: 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid(Non-covalent)

KD0.3: 23 residues within 4Å: Chain A: N.28, K.57, S.59, K.62, N.64, R.65, S.66, D.97, Q.115, K.140, H.204, Q.207, R.209, A.215, S.216, F.239, E.241, C.251, D.252 Chain C: R.122 Ligands: A5P.1, PEP.2, EDO.5 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.28, A:S.59, A:K.62, A:N.64, A:N.64, A:N.64, A:S.66, A:Q.115, A:Q.207, A:S.216, A:E.241, A:D.252 Water bridges: A:S.59, A:R.65, A:R.65, A:S.67, A:S.67, A:D.97, A:R.170, A:D.252 Salt bridges: A:K.57, A:K.62, A:R.65, A:K.140, A:H.204, A:R.209, C:R.122 KD0.8: 23 residues within 4Å: Chain B: N.28, K.57, S.59, K.62, N.64, R.65, S.66, D.97, Q.115, K.140, H.204, Q.207, R.209, A.215, S.216, F.239, E.241, C.251, D.252 Chain D: R.122 Ligands: A5P.6, PEP.7, EDO.10 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.28, B:S.59, B:K.62, B:N.64, B:N.64, B:N.64, B:S.66, B:D.97, B:Q.115, B:Q.207, B:S.216 Water bridges: B:S.67, B:R.170 Salt bridges: B:K.57, B:K.62, B:R.65, B:K.140, B:H.204, B:R.209, D:R.122 KD0.13: 23 residues within 4Å: Chain A: R.122 Chain C: N.28, K.57, S.59, K.62, N.64, R.65, S.66, D.97, Q.115, K.140, H.204, Q.207, R.209, A.215, S.216, F.239, E.241, C.251, D.252 Ligands: A5P.11, PEP.12, EDO.15 26 PLIP interactions: 24 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.28, C:S.59, C:K.62, C:N.64, C:N.64, C:S.66, C:Q.115, C:Q.207, C:S.216, C:E.241, C:D.252, A:R.122 Water bridges: C:S.59, C:R.65, C:R.65, C:S.67, C:D.97, C:R.170, C:D.252 Salt bridges: C:K.57, C:K.62, C:R.65, C:K.140, C:H.204, C:R.209, A:R.122 KD0.18: 22 residues within 4Å: Chain B: R.122 Chain D: N.28, K.57, S.59, K.62, N.64, R.65, S.66, D.97, Q.115, K.140, H.204, Q.207, R.209, A.215, S.216, F.239, E.241, C.251, D.252 Ligands: A5P.16, PEP.17 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.28, D:S.59, D:K.62, D:N.64, D:N.64, D:S.66, D:Q.115, D:Q.207, D:S.216, D:D.252 Water bridges: D:R.65, D:S.67, D:S.67, D:R.170, D:R.170, D:R.170, D:D.252, D:D.252 Salt bridges: D:K.57, D:K.62, D:R.65, D:K.140, D:H.204, D:R.209, B:R.122

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: N.17, F.186, R.187, V.198, G.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.186 Water bridges: A:N.17, A:G.234 EDO.5: 9 residues within 4Å: Chain A: F.119, Q.143, R.170, Q.207, R.209 Chain C: R.122 Ligands: A5P.1, PEP.2, KD0.3 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.143, A:R.170, A:R.170, A:Q.207, A:R.209, C:R.122, C:R.122 Water bridges: A:N.64, A:R.209 EDO.9: 6 residues within 4Å: Chain B: N.17, F.186, R.187, V.198, G.234, I.235 No protein-ligand interaction detected (PLIP) EDO.10: 9 residues within 4Å: Chain B: F.119, Q.143, R.170, Q.207, R.209 Chain D: R.122 Ligands: A5P.6, PEP.7, KD0.8 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain B Hydrogen bonds: D:R.122, D:R.122, B:R.170, B:Q.207, B:R.209, B:R.209 Water bridges: B:Q.143, B:Q.143, B:R.170 EDO.14: 8 residues within 4Å: Chain C: N.17, F.186, R.187, A.190, V.198, V.233, G.234, I.235 No protein-ligand interaction detected (PLIP) EDO.15: 9 residues within 4Å: Chain A: R.122 Chain C: F.119, Q.143, R.170, Q.207, R.209 Ligands: A5P.11, PEP.12, KD0.13 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.170, C:R.170, C:Q.207, C:R.209, A:R.122, A:R.122 Water bridges: C:N.64 EDO.19: 6 residues within 4Å: Chain D: N.17, F.186, R.187, V.198, G.234, I.235 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Combining functional and structural genomics to sample the essential Burkholderia structome. Plos One (2013)

Release Date

2011-11-30

Peptides

2-dehydro-3-deoxyphosphooctonate aldolase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2-dehydro-3-deoxyphosphooctonate aldolase 2

Related Entries With Identical Sequence