SMTL ID : 7su7.1

Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-octamer

Ligands

8 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 4 residues within 4Å: Chain A: E.32, V.53, N.131 Chain D: E.31 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.121, A:S.121, A:N.131 Water bridges: A:K.119, A:K.119 TRS.4: 3 residues within 4Å: Chain B: L.108, R.109, N.112 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.109 TRS.8: 4 residues within 4Å: Chain B: A.66, G.67 Chain D: R.98, E.102 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.102 TRS.9: 6 residues within 4Å: Chain D: E.32, V.53, S.121, P.123, K.130, N.131 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.32, D:S.121, D:S.121 Water bridges: D:K.51 TRS.10: 4 residues within 4Å: Chain E: E.32, V.53, N.131 Chain H: E.31 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.121, E:S.121, E:N.131 Water bridges: E:K.119, E:K.119 TRS.13: 3 residues within 4Å: Chain F: L.108, R.109, N.112 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.109 TRS.17: 4 residues within 4Å: Chain F: A.66, G.67 Chain H: R.98, E.102 No protein-ligand interaction detected (PLIP) TRS.18: 6 residues within 4Å: Chain H: E.32, V.53, S.121, P.123, K.130, N.131 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain F Hydrogen bonds: H:E.32, H:S.121, H:S.121 Water bridges: H:K.51, F:E.31

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 5 residues within 4Å: Chain A: S.34, I.36 Chain C: Q.128 Chain G: S.34, I.36 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A, 1 interactions with chain G Hydrogen bonds: C:Q.128, A:S.34, A:S.34 Hydrophobic interactions: A:I.36, G:I.36 Water bridges: A:S.34 MPD.11: 5 residues within 4Å: Chain C: S.34, I.36 Chain E: S.34, I.36 Chain G: Q.128 6 PLIP interactions: 4 interactions with chain E, 1 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: E:I.36, C:I.36 Hydrogen bonds: E:S.34, E:S.34, G:Q.128 Water bridges: E:S.34

8 x PH2: 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE(Non-covalent)

PH2.3: 15 residues within 4Å: Chain B: V.28, C.74, L.75, S.76, Y.77, A.78 Chain D: G.40, V.41, Y.42, E.45, A.94, L.95, V.96, E.97, K.122 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:V.41, D:E.45, D:V.96, D:K.122, B:L.75, B:Y.77, B:Y.77, B:A.78 Water bridges: D:E.97 Salt bridges: D:E.97 pi-Stacking: B:Y.77, B:Y.77 PH2.5: 13 residues within 4Å: Chain A: C.74, L.75, S.76, Y.77 Chain C: G.40, V.41, Y.42, E.45, A.94, L.95, V.96, E.97, K.122 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:L.75, A:Y.77, A:A.78, C:V.41, C:E.45, C:V.96, C:K.122 Water bridges: A:L.75, C:Y.42 pi-Stacking: A:Y.77, A:Y.77 Salt bridges: C:E.97 PH2.6: 13 residues within 4Å: Chain B: G.40, V.41, E.45, A.94, L.95, V.96, E.97, K.122 Chain C: C.74, L.75, S.76, Y.77, A.78 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:L.75, C:Y.77, C:Y.77, C:A.78, B:V.41, B:E.45, B:V.96, B:K.122 Water bridges: C:L.75, C:S.76 pi-Stacking: C:Y.77, C:Y.77 Salt bridges: B:E.97 PH2.7: 12 residues within 4Å: Chain A: G.40, V.41, E.45, A.94, L.95, V.96, E.97, K.122 Chain D: C.74, L.75, S.76, Y.77 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:L.75, D:Y.77, D:Y.77, A:V.41, A:E.45, A:V.96, A:K.122 Water bridges: D:S.76, A:E.97 pi-Stacking: D:Y.77, D:Y.77 Salt bridges: A:E.97 PH2.12: 15 residues within 4Å: Chain F: V.28, C.74, L.75, S.76, Y.77, A.78 Chain H: G.40, V.41, Y.42, E.45, A.94, L.95, V.96, E.97, K.122 12 PLIP interactions: 7 interactions with chain F, 5 interactions with chain H Hydrogen bonds: F:L.75, F:Y.77, F:Y.77, F:A.78, H:V.41, H:E.45, H:V.96, H:K.122 Water bridges: F:L.75 pi-Stacking: F:Y.77, F:Y.77 Salt bridges: H:E.97 PH2.14: 13 residues within 4Å: Chain E: C.74, L.75, S.76, Y.77 Chain G: G.40, V.41, Y.42, E.45, A.94, L.95, V.96, E.97, K.122 13 PLIP interactions: 5 interactions with chain G, 8 interactions with chain E Hydrogen bonds: G:V.41, G:E.45, G:V.96, G:K.122, E:L.75, E:Y.77, E:Y.77, E:A.78 Salt bridges: G:E.97 Water bridges: E:L.75, E:S.76 pi-Stacking: E:Y.77, E:Y.77 PH2.15: 13 residues within 4Å: Chain F: G.40, V.41, E.45, A.94, L.95, V.96, E.97, K.122 Chain G: C.74, L.75, S.76, Y.77, A.78 12 PLIP interactions: 6 interactions with chain F, 6 interactions with chain G Hydrogen bonds: F:V.41, F:E.45, F:V.96, F:K.122, G:L.75, G:Y.77, G:A.78 Water bridges: F:E.97, G:S.76 Salt bridges: F:E.97 pi-Stacking: G:Y.77, G:Y.77 PH2.16: 12 residues within 4Å: Chain E: G.40, V.41, E.45, A.94, L.95, V.96, E.97, K.122 Chain H: C.74, L.75, S.76, Y.77 12 PLIP interactions: 5 interactions with chain E, 7 interactions with chain H Hydrogen bonds: E:V.41, E:E.45, E:V.96, E:K.122, H:L.75, H:Y.77, H:Y.77 Salt bridges: E:E.97 Water bridges: H:L.75, H:S.76 pi-Stacking: H:Y.77, H:Y.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bourne, C.R., Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with product. To Be Published

Release Date

2022-12-28

Peptides

7,8-dihydroneopterin aldolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

7,8-dihydroneopterin aldolase

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