SMTL ID : 8oha.1 (1 other biounit)

Crystal structure of Leptospira interrogans GAPDH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-tetramer

Ligands

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 9 residues within 4Å: Chain A: D.197, R.199, P.210, A.211, S.212, M.233 Chain B: D.300, A.301, I.303 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.301, A:D.197 PEG.2: 1 residues within 4Å: Chain A: K.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.258 PEG.14: 9 residues within 4Å: Chain B: S.153, C.154, T.155, H.181, T.213, G.214, A.215, S.234, R.236 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.153, B:T.155, B:G.214, B:A.215, B:S.234, B:S.234, B:R.236 PEG.15: 3 residues within 4Å: Chain B: S.291, T.292, L.293 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Water bridges: D:R.54 Hydrogen bonds: B:T.292, B:T.292 PEG.16: 7 residues within 4Å: Chain B: Y.48, R.54 Chain D: T.279, F.288, S.291, L.293, I.296 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.48, B:Y.48, B:R.54, B:R.54, D:S.291 PEG.32: 4 residues within 4Å: Chain D: G.274, I.275, R.325, D.328 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.325

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: G.135, V.136, N.137, N.138, E.139 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: K.273, G.274, D.328 Ligands: GOL.6 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: K.164, V.165, D.168, N.169, A.267 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: G.270, A.271, M.272, K.273, I.275 Ligands: GOL.4 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: S.153, C.154, T.155, T.213, G.214, A.215 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: D.25, N.27, R.331 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: S.77, E.78, R.79 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: M.282, D.300 Chain B: D.197, P.210, S.212 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: A.185, P.188 Chain D: A.185 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain B: S.268, G.277, Y.278 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: G.135, V.136, N.137, N.138, E.139 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: L.167, D.168, G.171, K.253 Ligand excluded by PLIP GOL.20: 2 residues within 4Å: Chain B: G.228, K.229 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: L.167, G.171, I.172, T.252 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain A: F.198 Chain B: D.281, M.282 Chain D: Y.44 Ligands: GOL.38 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain C: K.273, G.274, D.328 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain C: C.154, T.155, T.179, H.181, T.213, S.234, R.236 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Chain C: T.255, S.256 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain A: R.54 Chain C: G.277, Y.278, F.288, L.293 Ligand excluded by PLIP GOL.31: 9 residues within 4Å: Chain C: D.197, R.199, P.210, A.211, S.212, M.233 Chain D: M.282, D.300, A.301 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain C: D.300 Chain D: D.197, R.199, P.210, A.211, S.212 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain D: S.153, T.155, H.181, T.213, S.234, R.236 Ligands: GOL.35 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain D: C.154, T.184, T.186, R.236 Ligands: GOL.34, NAD.40 Ligand excluded by PLIP GOL.36: 2 residues within 4Å: Chain D: G.57, T.58 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain C: M.282 Chain D: K.195, K.196, D.197, F.198 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain A: F.198 Chain D: D.40, Y.44, H.61 Ligands: GOL.22 Ligand excluded by PLIP

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

PO4.10: 4 residues within 4Å: Chain A: T.184, T.186, R.236 Ligands: NAD.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.186 Salt bridges: A:R.236 PO4.23: 5 residues within 4Å: Chain B: C.154, T.184, T.186, R.236 Ligands: NAD.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.184, B:T.184 Salt bridges: B:R.236 PO4.24: 4 residues within 4Å: Chain B: T.186, Q.187, D.197, R.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.186, B:T.186 Salt bridges: B:R.236 PO4.39: 7 residues within 4Å: Chain D: T.186, Q.187, D.197, G.200, I.209, A.211, R.236 2 PLIP interactions: 2 interactions with chain D Water bridges: D:P.210 Salt bridges: D:R.236

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.11: 23 residues within 4Å: Chain A: N.9, G.10, G.12, R.13, I.14, N.34, D.35, L.36, E.78, R.79, S.97, T.98, G.99, L.100, S.121, A.122, C.154, A.185, N.318, E.319, Y.322 Chain D: P.193 Ligands: PO4.10 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.14, A:Y.322 Hydrogen bonds: A:R.13, A:I.14, A:N.34, A:R.79, A:N.318 Water bridges: A:G.12, A:G.15, A:R.16, A:G.99, D:D.191 NAD.25: 24 residues within 4Å: Chain B: N.9, G.10, F.11, G.12, R.13, I.14, N.34, D.35, L.36, E.78, R.79, S.97, T.98, G.99, L.100, S.121, A.122, C.154, A.185, N.318, E.319, Y.322 Chain C: P.193 Ligands: PO4.23 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.14, B:Y.322 Hydrogen bonds: B:F.11, B:R.13, B:I.14, B:N.34, B:R.79, B:N.318 Water bridges: B:N.9, B:G.15, B:G.99, B:S.121 NAD.30: 21 residues within 4Å: Chain B: P.193 Chain C: N.9, G.10, G.12, R.13, I.14, N.34, D.35, L.36, E.78, R.79, S.97, T.98, G.99, L.100, S.121, A.122, C.154, A.185, N.318, Y.322 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.14, C:Y.322 Hydrogen bonds: C:R.13, C:I.14, C:N.34, C:R.79, C:N.318 Water bridges: C:R.16, C:A.185, C:A.185, B:D.191 NAD.40: 24 residues within 4Å: Chain A: P.193 Chain D: N.9, G.10, F.11, G.12, R.13, I.14, N.34, D.35, L.36, E.78, R.79, S.97, T.98, G.99, L.100, S.121, A.122, C.154, T.184, A.185, N.318, Y.322 Ligands: GOL.35 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.14, D:Y.322 Hydrogen bonds: D:R.13, D:I.14, D:N.34, D:R.79, D:N.318 Water bridges: D:N.9, D:G.12, D:G.99, D:S.121, D:A.185, D:A.185, D:T.186, D:E.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Navas-Yuste, S. et al., The structure of Leptospira interrogans GAPDH sheds light into an immunoevasion factor that can target the anaphylatoxin C5a of innate immunity. Front Immunol (2023)

Release Date

2023-08-23

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glyceraldehyde-3-phosphate dehydrogenase

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