SMTL ID : 6ok4.1

Crystal Structure of Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Chlamydia trachomatis with bound NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 21 residues within 4Å: Chain A: G.15, F.16, G.17, R.18, I.19, N.40, D.41, L.42, K.85, S.103, T.104, G.105, L.106, T.127, A.128, C.158, A.189, N.322, E.323, Y.326 Chain C: P.197 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.19, A:Y.326 Hydrogen bonds: A:F.16, A:R.18, A:I.19, A:N.40, A:K.85, A:N.322 Water bridges: A:N.14, A:F.16, A:G.17, A:R.21, A:G.105, A:T.127, A:A.189, A:E.323 NAD.9: 21 residues within 4Å: Chain B: N.14, G.15, F.16, G.17, R.18, I.19, N.40, D.41, L.42, E.84, K.85, S.103, T.104, G.105, L.106, T.127, A.128, C.158, A.189, N.322, Y.326 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.19, B:Y.326 Hydrogen bonds: B:F.16, B:R.18, B:I.19, B:N.40, B:T.127, B:N.322 Water bridges: B:R.21, B:R.21 NAD.17: 19 residues within 4Å: Chain C: G.15, F.16, G.17, R.18, I.19, N.40, D.41, L.42, S.103, T.104, G.105, L.106, T.127, A.128, C.158, A.189, N.322, E.323, Y.326 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.19, C:Y.326 Hydrogen bonds: C:F.16, C:R.18, C:I.19, C:N.40, C:T.127, C:N.322 Water bridges: C:N.14, C:G.17, C:E.84, C:G.105, C:A.189, C:A.189 NAD.26: 20 residues within 4Å: Chain D: N.14, G.15, F.16, G.17, R.18, I.19, N.40, D.41, L.42, S.103, T.104, G.105, L.106, T.127, A.128, C.158, A.189, N.322, E.323, Y.326 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.19, D:Y.326 Hydrogen bonds: D:F.16, D:R.18, D:I.19, D:N.322 Water bridges: D:R.21, D:R.21, D:T.188, D:A.189, D:E.323, B:D.195

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

EDO.2: 6 residues within 4Å: Chain A: P.135, T.136, F.137, N.142, L.225, C.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.136, A:N.142 EDO.3: 3 residues within 4Å: Chain A: K.254, R.312 Chain B: E.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.254, A:R.312 EDO.6: 4 residues within 4Å: Chain A: T.57, I.293 Chain D: T.57, I.293 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Water bridges: B:Q.210, D:G.59, C:Q.210 EDO.10: 6 residues within 4Å: Chain B: D.172, N.173, A.267, H.270, A.271, S.275 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.172, B:D.172, B:N.173, B:A.267, B:S.275 EDO.11: 6 residues within 4Å: Chain B: L.171, G.175, I.176, E.229, K.233, S.256 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.176, B:E.177, B:E.229, B:K.233, B:S.256, B:S.256 EDO.12: 4 residues within 4Å: Chain B: S.256, S.257, A.258, R.312 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.258, B:R.312, B:R.312 EDO.13: 3 residues within 4Å: Chain B: Y.261, A.303, G.306 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.304 EDO.14: 6 residues within 4Å: Chain A: Q.304, A.305 Chain B: D.201, R.203, P.214, A.215 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.201, B:R.203, A:Q.304 EDO.18: 4 residues within 4Å: Chain A: V.43 Chain C: P.197, S.198, R.199 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.199 Water bridges: C:S.198, C:S.198 EDO.19: 3 residues within 4Å: Chain C: K.200, D.201, W.202 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.200, C:W.202 Water bridges: C:R.203 EDO.20: 4 residues within 4Å: Chain C: K.254, D.311, R.312 Chain D: E.178 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.254, C:D.311 Water bridges: D:K.254, D:K.254 EDO.21: 4 residues within 4Å: Chain C: Y.261, C.265, A.303, Q.304 No protein-ligand interaction detected (PLIP) EDO.24: 4 residues within 4Å: Chain C: Y.261, G.306, V.307, A.308 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.308, C:A.308 EDO.27: 5 residues within 4Å: Chain D: P.135, T.136, F.137, N.142, L.225 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.136, D:N.142 EDO.28: 4 residues within 4Å: Chain D: S.256, S.257, A.258, R.312 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.258, D:R.312 Water bridges: D:R.312

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

PO4.4: 6 residues within 4Å: Chain A: S.157, T.159, T.160, T.217, G.218, A.219 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.157, A:T.217, A:T.217, A:G.218 Water bridges: A:C.158, A:T.159, A:T.160, A:G.218 PO4.5: 5 residues within 4Å: Chain A: E.178, K.254, R.312 Chain B: K.254, F.313 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.312, A:R.312 Salt bridges: A:K.254, B:K.254 Water bridges: B:K.254, B:K.254 PO4.15: 5 residues within 4Å: Chain B: S.157, T.159, T.217, G.218, A.219 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.157, B:T.159, B:T.160, B:T.217, B:T.217, B:G.218 PO4.22: 6 residues within 4Å: Chain C: S.157, T.159, T.160, T.217, G.218, A.219 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.157, C:T.159, C:T.217, C:T.217, C:T.217, C:G.218, C:A.219 Water bridges: C:T.160 PO4.23: 5 residues within 4Å: Chain C: E.178, K.254, R.312 Chain D: K.254, F.313 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:K.254, C:K.254 Hydrogen bonds: C:R.312, C:R.312 PO4.29: 6 residues within 4Å: Chain D: S.157, T.159, T.160, T.217, G.218, A.219 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.157, D:S.157, D:T.160, D:T.217, D:T.217, D:G.218 Water bridges: D:S.157, D:C.158, D:T.159

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

PEG.7: 6 residues within 4Å: Chain A: G.140, V.141, N.142, H.143, Q.144, Q.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.144, A:Q.145 PEG.16: 5 residues within 4Å: Chain B: V.141, N.142, H.143, Q.144, Q.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.143, B:Q.144, B:Q.145 PEG.25: 6 residues within 4Å: Chain C: G.140, V.141, N.142, H.143, Q.144, Q.145 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.144, C:Q.145 PEG.30: 6 residues within 4Å: Chain D: G.140, V.141, N.142, H.143, Q.144, Q.145 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.144

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: H.7, H.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barrett, K.F. et al., Structures of glyceraldehyde 3-phosphate dehydrogenase in Neisseria gonorrhoeae and Chlamydia trachomatis. Protein Sci. (2020)

Release Date

2019-04-24

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