SMTL ID : 9dq7.1

Borrelia burgdorferi LDH with NADH, oxamate and FBS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

4 x 6V0: [[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

6V0.1: 35 residues within 4Å: Chain A: I.10, G.11, A.12, G.13, G.14, V.15, G.16, I.36, D.37, V.38, N.39, K.42, Y.68, T.80, A.81, G.82, L.83, N.84, Q.85, L.94, N.98, I.101, D.104, I.105, A.121, S.122, N.123, V.125, T.146, L.150, H.178, A.230, T.231, I.235 Ligands: OXM.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.150, A:I.235, A:I.235 Hydrogen bonds: A:G.14, A:V.15, A:D.37, A:D.37, A:V.38, A:N.39, A:Y.68, A:G.82, A:L.83, A:L.83, A:N.84, A:N.98, A:N.123, A:N.123, A:T.146, A:T.146 Water bridges: A:G.16, A:N.84 6V0.4: 34 residues within 4Å: Chain B: I.10, G.11, A.12, G.13, G.14, V.15, G.16, I.36, D.37, V.38, N.39, K.42, Y.68, T.80, A.81, G.82, L.83, N.84, Q.85, N.98, I.101, D.104, I.105, A.121, S.122, N.123, V.125, T.146, L.150, H.178, A.230, T.231, I.235 Ligands: OXM.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.150, B:I.235 Hydrogen bonds: B:A.12, B:G.14, B:V.15, B:D.37, B:D.37, B:V.38, B:Y.68, B:G.82, B:N.84, B:N.98, B:A.121, B:N.123, B:N.123 Water bridges: B:G.13, B:G.16 6V0.9: 34 residues within 4Å: Chain C: I.10, G.11, A.12, G.13, G.14, V.15, G.16, I.36, D.37, V.38, N.39, Y.68, T.80, A.81, G.82, L.83, N.84, Q.85, N.98, I.101, D.104, I.105, A.121, S.122, N.123, V.125, T.146, G.147, L.150, H.178, A.230, T.231, I.235 Ligands: OXM.7 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.150, C:I.235 Hydrogen bonds: C:G.14, C:V.15, C:D.37, C:D.37, C:V.38, C:Y.68, C:Y.68, C:G.82, C:N.84, C:N.123, C:N.123, C:T.146, C:H.178 Water bridges: C:G.13, C:G.16 6V0.10: 34 residues within 4Å: Chain D: I.10, G.11, A.12, G.13, G.14, V.15, G.16, I.36, D.37, V.38, N.39, K.42, Y.68, T.80, A.81, G.82, L.83, N.84, Q.85, N.98, I.101, D.104, I.105, A.121, S.122, N.123, V.125, T.146, L.150, H.178, A.230, T.231, I.235 Ligands: OXM.11 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:L.150, D:I.235 Hydrogen bonds: D:G.13, D:G.14, D:V.15, D:D.37, D:V.38, D:G.82, D:N.84, D:N.98, D:A.121, D:N.123, D:N.123, D:T.146, D:H.178 Water bridges: D:G.16, D:K.42, D:Y.68, D:Q.85, D:Q.85

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 10 residues within 4Å: Chain A: Q.85, R.91, N.123, L.150, R.154, H.178, A.221, I.225, T.231 Ligands: 6V0.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.85, A:R.91, A:R.91, A:N.123, A:H.178, A:T.231, A:T.231 Salt bridges: A:R.91, A:R.154, A:H.178 OXM.5: 8 residues within 4Å: Chain B: N.123, L.150, R.154, H.178, A.221, I.225, T.231 Ligands: 6V0.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.123, B:T.231, B:T.231 Water bridges: B:A.221, B:T.231 Salt bridges: B:R.154, B:H.178 OXM.7: 10 residues within 4Å: Chain C: Q.85, R.91, N.123, L.150, R.154, H.178, A.221, I.225, T.231 Ligands: 6V0.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.85, C:R.91, C:R.91, C:N.123, C:H.178, C:T.231, C:T.231 Salt bridges: C:R.91, C:R.154, C:H.178 OXM.11: 10 residues within 4Å: Chain D: Q.85, E.89, N.123, L.150, R.154, H.178, A.221, I.225, T.231 Ligands: 6V0.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.85, D:N.123, D:H.178, D:T.231 Water bridges: D:A.221, D:T.231 Salt bridges: D:R.154, D:H.178

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: D.161, N.164 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.161, A:D.161, H2O.2 CA.12: 2 residues within 4Å: Chain D: D.161, N.164 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.161, D:D.161

2 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.6: 12 residues within 4Å: Chain B: R.156, Q.168, N.169, H.171, Y.173, A.192 Chain D: R.156, Q.168, N.169, H.171, Y.173, A.192 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:Q.168, B:N.169, D:R.156, D:Q.168, D:N.169 Salt bridges: B:R.156, B:H.171, B:H.171, D:R.156, D:H.171, D:H.171 FBP.8: 12 residues within 4Å: Chain A: R.156, Q.168, N.169, H.171, Y.173, A.192 Chain C: R.156, Q.168, N.169, H.171, Y.173, A.192 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:Q.168, A:N.169, C:R.156, C:N.169 Salt bridges: A:R.156, A:H.171, A:H.171, C:R.156, C:H.171, C:H.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lynch, M.J., Borrelia burgdorferi LDH with NADH, oxamate and FBS. To Be Published

Release Date

2025-03-12

Peptides

L-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
A

C
B

D
C

L-lactate dehydrogenase

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