SMTL ID : 6q94.3 (2 other biounits)

Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-Man

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 27 residues within 4Å: Chain A: G.10, T.12, G.13, Q.14, D.15, R.35, N.41, D.66, L.67, T.68, L.88, G.89, A.90, Q.91, S.92, Y.103, V.107, A.133, S.134, Y.159, K.163, H.189, R.194 Chain B: R.36, S.37, S.38 Ligands: GDD.2 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.12, A:T.12, A:Q.14, A:Q.14, A:D.15, A:N.41, A:L.67, A:L.88, A:A.90, A:S.92, A:Y.103, A:Y.103, A:Y.159, A:K.163, B:S.38, B:S.38, B:S.38, B:S.38 Salt bridges: A:R.35, B:R.36 pi-Cation interactions: A:R.35 NAP.4: 27 residues within 4Å: Chain A: R.36, S.37, S.38 Chain B: G.10, I.11, T.12, G.13, Q.14, D.15, R.35, N.41, D.66, L.67, T.68, L.88, G.89, A.90, Q.91, S.92, Y.103, V.107, A.133, S.134, T.135, Y.159, K.163 Ligands: GDD.5 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.10, B:T.12, B:T.12, B:G.13, B:Q.14, B:Q.14, B:D.15, B:N.41, B:D.66, B:L.67, B:L.88, B:A.90, B:S.92, B:Y.159, B:Y.159, B:K.163, A:S.38, A:S.38 Salt bridges: B:R.35, A:R.36 pi-Cation interactions: B:R.35 NAP.7: 27 residues within 4Å: Chain C: G.10, T.12, G.13, Q.14, D.15, R.35, N.41, D.66, L.67, T.68, L.88, G.89, A.90, Q.91, S.92, Y.103, V.107, A.133, S.134, Y.159, K.163, H.189, R.194 Chain D: R.36, S.37, S.38 Ligands: GDD.8 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:T.12, C:T.12, C:Q.14, C:Q.14, C:D.15, C:N.41, C:L.67, C:L.88, C:A.90, C:S.92, C:Y.103, C:K.163, D:S.38, D:S.38, D:S.38, D:S.38 Salt bridges: C:R.35, D:R.36 pi-Cation interactions: C:R.35 NAP.10: 27 residues within 4Å: Chain C: R.36, S.37, S.38 Chain D: G.10, I.11, T.12, G.13, Q.14, D.15, R.35, N.41, D.66, L.67, T.68, L.88, G.89, A.90, Q.91, S.92, Y.103, V.107, A.133, S.134, T.135, Y.159, K.163 Ligands: GDD.11 21 PLIP interactions: 3 interactions with chain C, 18 interactions with chain D Hydrogen bonds: C:S.38, C:S.38, D:G.10, D:T.12, D:T.12, D:G.13, D:Q.14, D:Q.14, D:D.15, D:N.41, D:D.66, D:L.67, D:L.88, D:A.90, D:S.92, D:Y.159, D:Y.159, D:K.163 Salt bridges: C:R.36, D:R.35 pi-Cation interactions: D:R.35

4 x GDD: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE(Non-covalent)

GDD.2: 24 residues within 4Å: Chain A: S.92, H.93, V.94, T.135, D.136, E.137, Y.159, L.186, F.187, N.188, R.194, N.197, F.198, V.199, K.202, L.220, G.221, N.222, A.225, R.227, Y.303, R.305, E.308 Ligands: NAP.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.92, A:T.135, A:T.135, A:L.186, A:N.188, A:R.194, A:R.194, A:N.197, A:V.199, A:K.202, A:G.221, A:R.305, A:E.308 Salt bridges: A:R.194, A:R.227, A:R.305, A:R.305 GDD.5: 24 residues within 4Å: Chain B: S.92, H.93, V.94, T.135, D.136, E.137, Y.159, F.187, N.188, R.194, N.197, F.198, V.199, K.202, L.220, G.221, N.222, A.225, R.227, Y.303, R.305, E.308, V.309 Ligands: NAP.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.92, B:D.136, B:N.188, B:R.194, B:R.194, B:N.197, B:V.199, B:K.202, B:G.221, B:N.222, B:R.305, B:E.308 Salt bridges: B:R.227, B:R.305, B:R.305 GDD.8: 24 residues within 4Å: Chain C: S.92, H.93, V.94, T.135, D.136, E.137, Y.159, L.186, F.187, N.188, R.194, N.197, F.198, V.199, K.202, L.220, G.221, N.222, A.225, R.227, Y.303, R.305, E.308 Ligands: NAP.7 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:S.92, C:T.135, C:T.135, C:Y.159, C:L.186, C:N.188, C:R.194, C:R.194, C:N.197, C:V.199, C:K.202, C:G.221, C:R.305, C:E.308 Salt bridges: C:R.194, C:R.227, C:R.305, C:R.305 GDD.11: 24 residues within 4Å: Chain D: S.92, H.93, V.94, T.135, D.136, E.137, Y.159, F.187, N.188, R.194, N.197, F.198, V.199, K.202, L.220, G.221, N.222, A.225, R.227, Y.303, R.305, E.308, V.309 Ligands: NAP.10 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.92, D:D.136, D:N.188, D:R.194, D:R.194, D:N.197, D:V.199, D:K.202, D:G.221, D:N.222, D:R.305, D:E.308 Salt bridges: D:R.227, D:R.305, D:R.305

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

EDO.3: 5 residues within 4Å: Chain A: F.40, H.55 Chain B: A.196, R.205 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: Y.64 Chain B: K.202, Y.303 Ligands: EDO.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.64, A:Y.64, B:K.202 EDO.9: 5 residues within 4Å: Chain C: F.40, H.55 Chain D: A.196, R.205 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain C: Y.64 Chain D: K.202, Y.303 Ligands: EDO.9 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.202, D:Y.303, C:Y.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pfeiffer, M. et al., A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase. Acs Catalysis (2019)

Release Date

2019-04-24

Peptides

GDP-mannose 4,6 dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
G

D
H

GDP-mannose 4,6 dehydratase

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