SMTL ID : 5a29.1

Family 2 Pectate Lyase from Vibrio vulnificus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.133, E.154, H.196 Chain B: H.5, H.7 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.133, A:E.154, A:H.196, B:H.5, B:H.7, H2O.6

3 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.2: 11 residues within 4Å: Chain A: I.234, Y.270, K.271, P.281, V.282, I.335, N.339, A.340, E.343, V.359, A.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.282, A:N.339 Salt bridges: A:K.271, A:K.271 SRT.15: 10 residues within 4Å: Chain A: L.231, F.233, N.302, S.303, R.308, Y.398 Chain B: H.5, H.6, H.7, S.8 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.303, A:R.308, A:R.308, B:H.7 Salt bridges: A:R.308, B:H.6, B:H.6, B:H.7 SRT.16: 10 residues within 4Å: Chain A: K.156, S.330, K.333 Chain B: S.8, S.9, G.10, L.11, V.12, R.14, H.17 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:G.10, B:L.11, B:V.12, B:V.12, A:S.330, A:S.330 Salt bridges: B:H.17, A:K.156, A:K.333 Water bridges: A:N.157, A:N.157, A:K.333, A:N.338

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

EDO.3: 8 residues within 4Å: Chain A: L.155, F.180, H.184, G.194, R.195, A.236, D.239, L.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.155, A:R.195, A:R.195 EDO.4: 7 residues within 4Å: Chain A: L.418, R.422, F.471, I.474, E.475, Q.478, T.527 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.422, A:F.471, A:E.475 Water bridges: A:T.536 EDO.5: 3 residues within 4Å: Chain A: G.194, R.195, H.196 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.186, A:R.195, A:H.196 Water bridges: A:E.186, A:M.193 EDO.6: 9 residues within 4Å: Chain A: Q.88, N.89, R.92, H.158, Y.159, L.543, S.544, G.545, S.546 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.89, A:R.92, A:L.543, A:G.545 Water bridges: A:A.85, A:N.89, A:H.158 EDO.7: 6 residues within 4Å: Chain A: Y.512, T.562, Y.566, K.567 Chain B: R.14, G.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.512, A:Y.512, B:G.15 EDO.8: 4 residues within 4Å: Chain A: Y.161, P.163, F.164, H.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.163 Water bridges: A:H.167 EDO.9: 3 residues within 4Å: Chain A: D.204, K.206, R.210 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.204, A:R.210 EDO.10: 6 residues within 4Å: Chain A: A.347, N.351, D.352, A.353, R.356, L.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.356 Water bridges: A:N.351 EDO.11: 6 residues within 4Å: Chain A: L.344, H.345, E.348, R.422, R.425, P.541 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.344, A:E.348, A:R.425 Water bridges: A:R.422 EDO.12: 7 residues within 4Å: Chain A: F.208, H.209, R.210, I.212, G.258, A.261, W.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.208 EDO.13: 4 residues within 4Å: Chain A: Y.367, Y.371, E.431, L.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.431 Water bridges: A:Y.367, A:Y.371 EDO.14: 5 residues within 4Å: Chain A: S.447, G.449, K.455, P.456, T.457 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.456, A:T.457 Water bridges: A:N.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mclean, R. et al., Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2. J.Biol.Chem. (2015)

Release Date

2015-07-01

Peptides

EXOPOLYGALACTURONATE LYASE: A
PECTATE LYASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

EXOPOLYGALACTURONATE LYASE

PECTATE LYASE